Temporary closure notices were placed on the shellfish beds after high E.coli bacteria readings last week.
Latest tests have showed satisfactory water quality levels, said the FSA.
Closures remain in place in Devon at Slapton, Taw and Torridge and in Jersey.
An FSA spokesman said: "Recent tests have shown high levels of E.coli contamination in 30 shellfish beds in Cornwall and Devon.
"However, a number of factors have led us to question circumstances which may have led to these unusual results, including the unprecedented nature of the results, the lack of a clear cause and the fact that other testing does not support the view that there is an obvious risk to public health.
"Because of this, the FSA will not follow its normal protocol and in this case will allow the closed shellfish beds to re-open as long as there is one further test that shows the bed has E coli within accepted tolerance levels."

Clive Weatherhogg set up meetings between the woman and a man he found through an adult website, and filmed them having sex.
A court heard he sent a message containing a sexually explicit clip to the victim's sister on Christmas Day.
Weatherhogg, 42, was also placed on the sex offenders register.
He had denied the charges but was found guilty following a trial at Dundee Sheriff Court.
Sheriff George Way remitted the case to the High Court in Edinburgh to be dealt with because its greater sentencing powers.
Weatherhogg, formerly of Guthrie, near Forfar, was found guilty of coercing the woman to engage in sexual activity and intercourse with the man between 10 September, 2013 and 17 September the following year.
He was also convicted of intentionally causing the woman's sister and father to look at sexual images and behaving in a threatening or abusive manner on 25 December, 2014.
The woman told the trial she had felt "blackmailed" by Weatherhogg.
Lady Wolffe told the Weatherhogg that she had to pass a sentence on him that "reflected society's abhorrence" at such conduct.
The judge said that Weatherhogg, a first offender, had been assessed as posing "a moderate risk" of sexual re-offending.
Defence counsel Jonathan Crowe said it had been "a dramatic shock" for Weatherhogg to be placed on remand ahead of sentencing.
Shellfish farms on the Helford River and Camel Estuary in Cornwall have re-opened after pollution closure notices were lifted by the Food Standards Agency (FSA).
[NEXT_CONCEPT]
A man who coerced a woman into having sex with a stranger before sending "revenge porn" to her family has been jailed for six years.