Conflict between the chief executive officer and national executive has gripped the Australian Federal Police Association, which represents federal and ACT police, for several months.

Tensions began to escalate after former AFPA national president Jon Hunt-Sharman resigned during a federal court case over election processes and conflict between national executive members.

Chief executive officer Dennis Gellatly is now refusing to recognise the new national president, Senior Constable Angela Smith, and is questioning the legality of her appointment by the association's national executive in November.

The stand-off came to a head in early December, when police were called to respond to a disturbance at the AFPA's office in Griffith.

Ms Smith, the new president, had attempted to enter the offices with Police Federation of Australia chief executive Mark Burgess. It is understood they were blocked by employees, who rang police.

The dispute comes at a crucial time for the association's members, which is about to move into negotiations for its next enterprise agreement.

In a further sign of the strained relations within the AFPA, it can be revealed that the national executive and chief executive were fighting over access to the association's bank accounts.

In an email to AFPA members just before Christmas. Ms Smith said the bank issues were being resolved.

"The national executive is also attempting to resolve access issues to all AFPA bank accounts with the CEO and remain hopeful this can be amicably resolved in the near future," she wrote.

"We are determined to ensure the management of our financial affairs is in accordance with AFPA rules, other regulatory requirements, and the general high standards you as members would expect."

It is understood the access issues have since been mostly resolved.

Mr Gellatly told Fairfax Media the bank account problems arose from a dispute over which members could access the union's accounts and authorise payments under the association's rules.

It had left the organisation in a position where it was unable to pay bills for several weeks, he said.

Mr Gellatly said a number of employees had resigned in the wake of the incident at the union's Griffith office in December.

But Ms Smith, in her December 23 email, said she had only received one formal notice of resignation from an employee who was already looking for another job before the Griffith stand-off.

The president told her members there was a high attrition rate within the union over the past 12 months, and that the national executive would be filling positions in the national office.

They had also brought in a former president of the Northern Territory Police Association, Vince Kelly, to assist.

"The CEO has not at this stage formally communicated with the national executive in relation to his future intentions," she wrote.

"Until such time as he does so we will manage the organisation as we are obliged to do under our rules."

Mr Gellatly has written to Fair Work Australia about the ongoing turmoil and urged them to investigate.