Parts of the sector expressed concern that the national charity regulator's future was again at risk after last week's announcement that Commissioner Susan Pascoe's position would end on September 30.

The Coalition had previously attempted to scrap the commission, but reversed its position in March last year.

The Community Council for Australia penned an open letter addressed to Prime Minister Malcolm Turnbull and delivered to Assistant Minister Michael Sukkar on Friday that called for Ms Pascoe to be reappointed for at least another 12 months.

The extended tenure, the letter argued, would allow the commission's five-year review to be conducted "without excluding her extensive knowledge and experience of how the organisation operates and performs".

"Failing this reappointment, we would like you to ensure there is a transparent, fair and consultative process to appoint the best possible replacement," the letter said.

"Given what has happened with Commissioner Pascoe, it is very difficult for the sector to have any confidence that the new appointment process will reflect the need for a strong, effective, independent charities regulator."

University of NSW Centre for Social Impact chief executive Kristy Muir, whose organisation has worked with the commission to develop the Australian Charities Report each year, said Ms Pascoe's tenure had ensured confidence from the sector.

"This is the first time that we've really had a good idea of the size and scope of the not-for-profit sector," she said.

"It's really started to deliver on building public trust, increasing transparency around what the sector does and accountability."

Ms Muir said the loss of the commission could result in the erosion of trust in the sector that had been built during the regulator's tenure.

"I think Susan Pascoe has been an exceptional leader as commissioner and she has helped to build trust in the commission across the sector," she said.

Mr Sukkar told Fairfax Media he had thanked Ms Pascoe for her service and said the search for the next commissioner would be transparent.

"The government greatly appreciates her service as the inaugural Commissioner as well as the experience she brought to the ACNC," he said.

"We will be undertaking an open and transparent merit-based selection process to fill the position of commissioner. This is standard practice in hiring heads of agencies."

Opposition Charities and Not-for-Profits spokesman Andrew Leigh said previous uncertainty about the commission "placed considerable stress on the organisation".

"It took a concerted campaign, including a letter from more than 40 major charities, before the Coalition finally withdrew their legislation to scrap the charities commission," he said.

"Australia's charities are now looking to see whether Michael Sukkar and the Turnbull government take our charities seriously."