Israeli scholars are furious after new flooring was fitted 'behind their backs' by the Muslim authority in charge of Judaism's holiest site - potentially covering up clues to the location of the 'Lost Ark'. The work at the Dome of the Rock was simply meant to replace carpet, worn away by thousands of pilgrims at the gold-topped shrine, which overlooks old Jerusalem. But when the old carpet was lifted, it revealed previously undocumented ancient floor designs - which could point to where the gold-cased Ark of the Covenant was buried 2,500 years ago. The discovery of the cryptic geometric patterns immediately caught the attention of some researchers, thrilled at the possibility of solving the Indiana Jones-type mystery which touches upon a holy grail for biblical enthusiasts. Scroll down for video . Hidden: Workers place carpets over ancient floor designs in the cave under the Dome of the Rock, which Israeli scholars are angry they did not get the chance to document before they were covered . Legend: Scholars have suggested the flooring may give a clue as to where the Ark of the Covenant - imagined here in the 1981 Indiana Jones film - is hidden, which Jewish tradition says is buried under the Dome . 'Something is there. I don't know what. But something is hidden there,' said Israeli archaeologist Zachi Dvira, who studies the site. Yet it looks likely it will remain a mystery: scholars did not get the chance to document the designs before workmen began laying the new carpet, paid for by King Abdullah II of Jordan, the country which remains the custodian of the area's Muslim holy sites. It has sparked a war of words between the Waqf, the Muslim authority that administers the Al Aqsa Mosque compound, which includes the Dome of the Rock, and Israeli archaeological authorities, who say the repairs were carried out behind their backs. The scholars also fear the glue being used may permanently damage the floor. Israel's housing minister Uri Ariel, of the nationalist Jewish Home party, waded in to the argument to urge an immediate halt to the work. In an alarmed letter sent to Prime Minister Benjamin Netanyahu last week, he wrote: 'There is no need to elaborate on how important this site is, where every modification, every excavation with heavy equipment can cause irreparable harm to the foundations of the Temple.' Row: The Dome of the Rock is one of the most contentious religious spots in all of Jerusalem, and the argument over the carpet is simply the latest in a long line of battle between Muslim and Jewish groups . Holy: The Dome of the Rock and its hilltop plaza is considered Judaism's holiest spot and Islam's third holiest . But the Waqf reject the accusations. Sheikh Azzam Tamimi, the head of the Waqf, said the work is long overdue and has defiantly proclaimed that he was forbidding any Israeli involvement. 'Our work in Al Aqsa is transparent,' he said. 'We are only putting down carpet and felt. Nothing more, nothing less.' They also deny the work will cause any damage. Jamal Al Quda, a member of a group of Jordanian carpet layers who received Israeli visas for the job,  said it was necessary to affix the base layer of thin dark felt before rolling out the carpet above it. 'It comes off my hand,' he added, rubbing his fingers. Heritage: The Dome is thought to be one of the most interesting archaeological sites in Jerusalem . Finance: This latest work, pictured last Sunday, is being paid for by King Abdullah II of Jordan . This is not the first time tensions have flared over work at the Dome of the Rock. The Dome of the Rock is at the centre of competing claims. Muslims believe it enshrines the large rock slab where Muslim tradition says the Prophet Muhammad ascended to heaven. Meanwhile, Jews believe the rock may be where the holiest part of the two ancient Temples stood as early as about 3,000 years ago — and where religious Jews pray a third Temple will one day be built. Ancient Jewish traditions say the Ark of the Covenant. which contained the Ten Commandments, may have been hidden away in a chamber when the First Jewish Temple was destroyed. The adjacent Western Wall, believed to be one of the last remnants of the Temple complex, is the holiest site where Jews can pray. But Palestinian officials reject Jewish historical ties to the site and the competing claims have been known to spill over into violence. While Jerusalem may be the most excavated city in the world, the Dome and its hilltop plaza are an archaeological goldmine which has never been properly dug because of the political sensitivities surrounding the site, which is considered Judaism's holiest spot and Islam's third holiest. In 1999, the Muslim authorities who administer the site dug an enormous hole 12 metres, or 40 feet, deep as part of construction for an underground prayer area, dumping 10,000 tons of earth in a nearby valley and an east Jerusalem dump. The director of the Israeli Antiquities Authority at the time called it an 'archaeological crime'. For years, Dvira and veteran Israeli archaeologist Gabriel Barkay have been leading a team of archaeologists and volunteers in combing through the dirt for historical finds. The initiative, called the Temple Mount Sifting Project, is conducted under the auspices of the Elad Foundation, a group that also purchases Arab homes in contested parts of East Jerusalem and helps move Jews in. Critics say this nationalist agenda should not mix with archaeology. Israel's state comptroller wrote a scathing report in 2010 about the Muslim authorities' illicit work projects at the compound and Israel's failure at enforcing supervision there. Israeli officials kept the report classified out of concern that its publication could harm the sensitive relationship with Jordan. Tens of thousands of worshippers attend weekly Friday prayers, and the carpets have been replaced before — most recently 12 years ago, at a time of heightened violence when Israeli antiquities officials were granted limited access to the site. Social media: Leaked photos of the work have fuelled this latest argument between the two sides . Past renovation projects were done quietly behind the scenes. Leaked photos posted on social media sites — combined with the political influence of Israeli nationalists monitoring the site — drew extra attention and fuelled the latest controversy. Photos that were leaked to Facebook from the off-limits restoration site showed a number of geometric floor patterns never before documented by archaeologists, said Frankie Snyder, a researcher with the Temple Mount Sifting Project. Some apparently date to when the Crusaders controlled the complex in the 12th century, she said. 'I'm worried about damage of the original floors,' said Barkay, the archaeologist. 'The patterns were never properly documented.' Israel Hasson, the director of the Israeli Antiquities Authority, said once the government body learned about the renovation, it made arrangements with the Waqf to send an archaeologist to document some of the floor patterns, but others already had been covered by the maroon and beige carpeting. 'We got to part of them. We didn't get to it all. I won't ask anyone to pull up the carpets to document it,' Hasson said. 'We will wait for the next opportunity. We're sure to be here over the next 2,000 years.'
Row erupted after mysterious geometric designs discovered under carpet . Some hope they may lead to chamber where Ark of the Covenant is hidden . But new flooring laid before Israeli scholars were able to document pattern . But Waqf, the authority in charge of Dome of the Rock, reject accusations .