CANBERRA, Feb 16 AAP - The federal government will pull its funding from the Islamic College of South Australia once the first term finishes in April.

Education Minister Simon Birmingham said the decision had not been taken lightly but the school had been given several chances since November 2015 and still did not meet the government's expectations.

"It is frustrating that after all this time the school is again in a situation where there have been multiple resignations from the board as recently as last week - including the resignation of the principal," Senator Birmingham said on Thursday.

There has been constant turnover of board members at the SA school since 2015 and it has missed a number of reporting deadlines the government requires.

The school received $4 million in commonwealth funding in 2016.

The government has already stripped funding from the Malek Fahd Islamic School in NSW, a decision upheld by the Administrative Appeals Tribunal in January, over similar governance and financial concerns.

In December it also asked the authority responsible for the Islamic College of Canberra to explain why it too should not lose federal funding after failing to meet standards.