Although the experimental protocol had not been published, physicists in several countries attempted, and failed, to replicate the excess heat phenomenon. The first paper submitted to Nature reproducing excess heat, although it passed peer review, was rejected because most similar experiments were negative and there were no theories that could explain a positive result; this paper was later accepted for publication by the journal Fusion Technology. Nathan Lewis, professor of chemistry at the California Institute of Technology, led one of the most ambitious validation efforts, trying many variations on the experiment without success, while CERN physicist Douglas R. O. Morrison said that "essentially all" attempts in Western Europe had failed. Even those reporting success had difficulty reproducing Fleischmann and Pons' results. On 10 April 1989, a group at Texas A&M University published results of excess heat and later that day a group at the Georgia Institute of Technology announced neutron production—the strongest replication announced up to that point due to the detection of neutrons and the reputation of the lab. On 12 April Pons was acclaimed at an ACS meeting. But Georgia Tech retracted their announcement on 13 April, explaining that their neutron detectors gave false positives when exposed to heat. Another attempt at independent replication, headed by Robert Huggins at Stanford University, which also reported early success with a light water control, became the only scientific support for cold fusion in 26 April US Congress hearings. But when he finally presented his results he reported an excess heat of only one degree Celsius, a result that could be explained by chemical differences between heavy and light water in the presence of lithium. He had not tried to measure any radiation and his research was derided by scientists who saw it later. For the next six weeks, competing claims, counterclaims, and suggested explanations kept what was referred to as "cold fusion" or "fusion confusion" in the news.
In April 1989, Fleischmann and Pons published a "preliminary note" in the Journal of Electroanalytical Chemistry. This paper notably showed a gamma peak without its corresponding Compton edge, which indicated they had made a mistake in claiming evidence of fusion byproducts. Fleischmann and Pons replied to this critique, but the only thing left clear was that no gamma ray had been registered and that Fleischmann refused to recognize any mistakes in the data. A much longer paper published a year later went into details of calorimetry but did not include any nuclear measurements.
Nevertheless, Fleischmann and Pons and a number of other researchers who found positive results remained convinced of their findings. The University of Utah asked Congress to provide $25 million to pursue the research, and Pons was scheduled to meet with representatives of President Bush in early May.
On 30 April 1989, cold fusion was declared dead by The New York Times. The Times called it a circus the same day, and the Boston Herald attacked cold fusion the following day.
On 1 May 1989, the American Physical Society held a session on cold fusion in Baltimore, including many reports of experiments that failed to produce evidence of cold fusion. At the end of the session, eight of the nine leading speakers stated that they considered the initial Fleischmann and Pons claim dead, with the ninth, Johann Rafelski, abstaining. Steven E. Koonin of Caltech called the Utah report a result of "the incompetence and delusion of Pons and Fleischmann," which was met with a standing ovation. Douglas R. O. Morrison, a physicist representing CERN, was the first to call the episode an example of pathological science.
On 4 May, due to all this new criticism, the meetings with various representatives from Washington were cancelled.
From 8 May, only the A&M tritium results kept cold fusion afloat.
In July and November 1989, Nature published papers critical of cold fusion claims. Negative results were also published in several other scientific journals including Science, Physical Review Letters, and Physical Review C (nuclear physics).
In August 1989, in spite of this trend, the state of Utah invested $4.5 million to create the National Cold Fusion Institute.
The United States Department of Energy organized a special panel to review cold fusion theory and research. The panel issued its report in November 1989, concluding that results as of that date did not present convincing evidence that useful sources of energy would result from the phenomena attributed to cold fusion. The panel noted the large number of failures to replicate excess heat and the greater inconsistency of reports of nuclear reaction byproducts expected by established conjecture. Nuclear fusion of the type postulated would be inconsistent with current understanding and, if verified, would require established conjecture, perhaps even theory itself, to be extended in an unexpected way. The panel was against special funding for cold fusion research, but supported modest funding of "focused experiments within the general funding system". Cold fusion supporters continued to argue that the evidence for excess heat was strong, and in September 1990 the National Cold Fusion Institute listed 92 groups of researchers from 10 countries that had reported corroborating evidence of excess heat, but they refused to provide any evidence of their own arguing that it could endanger their patents. However, no further DOE nor NSF funding resulted from the panel's recommendation. By this point, however, academic consensus had moved decidedly toward labeling cold fusion as a kind of "pathological science".
In March 1990, Michael H. Salamon, a physicist from the University of Utah, and nine co-authors reported negative results. University faculty were then "stunned" when a lawyer representing Pons and Fleischmann demanded the Salamon paper be retracted under threat of a lawsuit. The lawyer later apologized; Fleischmann defended the threat as a legitimate reaction to alleged bias displayed by cold-fusion critics.
In early May 1990, one of the two A&M researchers, Kevin Wolf, acknowledged the possibility of spiking, but said that the most likely explanation was tritium contamination in the palladium electrodes or simply contamination due to sloppy work. In June 1990 an article in Science by science writer Gary Taubes destroyed the public credibility of the A&M tritium results when it accused its group leader John Bockris and one of his graduate students of spiking the cells with tritium. In October 1990 Wolf finally said that the results were explained by tritium contamination in the rods. An A&M cold fusion review panel found that the tritium evidence was not convincing and that, while they couldn't rule out spiking, contamination and measurements problems were more likely explanations, and Bockris never got support from his faculty to resume his research.
On 30 June 1991, the National Cold Fusion Institute closed after it ran out of funds; it found no excess heat, and its reports of tritium production were met with indifference.
On 1 January 1991, Pons left the University of Utah and went to Europe. In 1992, Pons and Fleischmann resumed research with Toyota Motor Corporation's IMRA lab in France. Fleischmann left for England in 1995, and the contract with Pons was not renewed in 1998 after spending $40 million with no tangible results. The IMRA laboratory stopped cold fusion research in 1998 after spending £12 million. Pons has made no public declarations since, and only Fleischmann continued giving talks and publishing papers.
Mostly in the 1990s, several books were published that were critical of cold fusion research methods and the conduct of cold fusion researchers. Over the years, several books have appeared that defended them. Around 1998, the University of Utah had already dropped its research after spending over $1 million, and in the summer of 1997, Japan cut off research and closed its own lab after spending $20 million.