The complaint will be filed with the National Anti-Corruption Commission after the Songkran holidays, said Anusorn Iamsa-ard, the party's deputy spokesperson.
Narong Sahamethapat was presented with the gift from Suthep Thaugsuban, who led the protesters to the Public Health Ministry on Tuesday.
Section 103 of the 1999 Organic Act on Counter Corruption prohibits an official from receiving a gift from unrelated persons when it is not a gift-giving occasion.
During such occasions, he may accept the gift, but its value may not exceed 3,000 baht.
Dr Narong said the gift was not for him alone and he simply accepted it on behalf of all officials at the ministry.
"If the whistle is worth 20,000 baht, the gift amounts to less than one baht for each of the 200,000 officials of the ministry," he argued.
"If we count only those coming up to greet Mr Suthep, the gift is no more than 3,000 baht each anyway," he said.
He stressed the whistle belonged to all public health officials and "we will keep it among the ministry's souvenirs".