Alpha radiation was detected in a sample of sludge from a drain upstream of the site on July 10 and reported to a sub-committee of the local stakeholder group on Wednesday evening. It was confirmed on Friday by DSRL, the private consortium that is cleaning up Dounreay.
According to the Government watchdog, the Scottish Environment Protection Agency (Sepa), a "small quantity of radioactivity" had been found by DSRL.
"The sample was taken from a manhole within a foul drain system, upstream of the Dounreay site," said a Sepa spokeswoman. "Following the initial notification DSRL has been undertaking subsequent analysis work to determine the source of the radioactivity.
"Sepa is in regular contact with DSRL, and it will continue to update us."
DSRL confirmed the manhole was part of an off-site drainage system which pre-dated the site and was now redundant.
"Samples of sludge were taken from the manhole that indicated elevated levels of alpha activity," said a company spokeswoman.
"We have agreed with Sepa we will obtain further samples and subject them to detailed analysis to confirm the level and source of the radioactivity.
"The results are expected mid-August."
The spokeswoman declined to say whether the pollution included plutonium, a radioactive heavy metal that emits alpha particles and has been made at Dounreay.
She said: "Although we are investigating the possibility the activity in the manhole may have come from sludges produced at the Shebster water treatment plant upstream of the manhole.
"DSRL will report on the findings once all the analysis has been complete."
The current clean-up bill for Dounreay, where failed fast breeder reactors were developed for 40 years until 1994, is £1.6 billion.