The comments come following reports that the FRA may have broken the law in carrying out telecom and internet surveillance, according to documents obtained by the daily Dagens Nyheter.
During the visit of US President Barack Obama, Swedish Foreign Minister Carl Bildt rejected criticism of Swedish surveillance of ordinary citizens claiming that his government has ensured it was "regulated by law".
However documents from SIUN, the state agency which inspects military intelligence in Sweden, reveal that the agency has criticized how the FRA handles data regarding the general public.
Earlier this year Metro newspaper reported on a SIUN investigation which pointed out that the FRA stores personal date for more than the legal 12 months, carrying out longer term surveillance than allowed by legislation.
"By moving the details between databases they get around the rules that require information to be deleted," law professor Mark Klamberg told the newspaper.
Last week the British journalist Duncan Campbell told an inquiry in the UK that Sweden's FRA is the most significant partner of the UK intelligence agency GCHQ, due to the country's strategic location.
The FRA has issued a statement saying that the organization requests an investigation by SIUN into what kind of cooperation is allowed with other countries.
"Given the picture which has been painted in the media we think it is important for us and for the general public to shed more light on this area," said FRA director Christina Malm.