The Australian Federal Police (AFP) pushed political propaganda on its criminal investigation database by inserting pop-ups on the internal system, the union representing officers has said.

The messages, which had to be acknowledged before proceeding, encouraged members to vote for a new enterprise agreement by offering an immediate pay rise - a proposal which was later defeated.

The union said it was removed within four hours after a flood of complaints.

"Members were horrified that someone saw fit to use the operational system to push this industrial message and it's a blatant misuse of that system," AFP Association (AFPA) president Angela Smith said.

"Our phones melted down. Emails, texts, Facebook. It just went berserk."

Ms Smith described the tactic as an "unbelievable dirty trick" to shore up votes.

"You cannot use an operational policing system for political propaganda. You just can't do it," she said.

The AFP acknowledged using the system was "an error of judgement" in a statement to the ABC.

"The item was removed well before there was any contact from the AFPA on the matter," the statement read.

Staff overwhelmingly reject offer

Late on Monday, staff overwhelmingly voted against the pay offer made by the AFP.

More than 80 per cent of staff who voted were opposed to the deal.

Ms Smith said the offer would have stripped AFP members of leave entitlements and other pay and conditions.

The AFPA will now restart negotiations on staff pay.