The AFP asked two government ministers to provide statements over media leaks about union raids at least twice, but they refused, a Senate inquiry has heard.
Australian Federal Police believe evidence could have been destroyed in relation to media leaks about union raids.
AFP deputy commissioner Leanne Close said officers investigating raids on Australian Workers' Union offices in 2017 found some instances in which evidence may have been destroyed.
"We did find some of that material may have been destroyed," Ms Close told a Senate estimates hearing in Canberra on Monday.
The committee also heard federal government ministers Michaelia Cash and Michael Keenan twice refused to provide witness statements to police.
Ms Close said both ministers were asked at least twice to explain their involvement in the raids.
"We wanted to have the opportunity to speak to them both," she said.
"We would've liked to have spoken to them and obtained a witness statement, as we would have preferred from the other (six) witnesses who didn't provide a witness statement to us."
Instead, both ministers sent the AFP letters to explain their roles.
The AFP provided Commonwealth prosecutors with a brief of evidence against one person in order to lay charges.
However, prosecutors decided there was insufficient evidence.
"In this case, the Commonwealth DPP determined that despite our best efforts the brief did not have sufficient prospects of success for them to prosecute," AFP Commissioner Andrew Colvin said.
"Under those circumstances, the AFP could not in good conscience lay charges."
Prosecutors must establish conviction prospects "beyond reasonable doubt" before pressing on with a case.
"It's a high bar and the CDPP took the view that the brief in this matter did not reach that bar," Mr Colvin said.
He acknowledged the AFP had seen evidence in relation to the union raids during an ongoing Federal Court trial, but said his officers could not compel people to self-incriminate.
"This is not an option open to police in a criminal investigation," he said.
"Ultimately, we cannot compel people to provide us with statements. Indeed, it may surprise you to know, that we cannot compel people to assist with our investigations or inquiries."
The October 2017 raids on AWU offices in Melbourne and Sydney shot to prominence when media were tipped off by staffers from Senator Cash's office and arrived before police.
The raids were launched in connection with decades-old donations made when Opposition Leader Bill Shorten was the AWU national secretary.
Senator Cash has consistently denied the raids were politically motivated.
Asked in parliament whether he could confirm two ministers had declined to provide witness statements to the AFP, Prime Minister Scott Morrison said the matter was before the courts.
"I do not intend to provide any comment other than to remind the house as to what this matter is all about and that is - why the leader of the opposition won't explain to the Australian people why union fund monies went to GetUp," Mr Morrison said.
Mr Colvin again expressed his disappointment about the union raids being leaked to the media.
"This is an issue of grave concern to me when AFP operational activity is inappropriately disclosed," he said.
"As well as the impact on our operations, these disclosures also jeopardise the safety and security of AFP officers."