Indonesian President Joko Widodo's portrait has been removed from the walls of the National Portrait Gallery to avoid being defaced  following the executions of Bali nine pair Andrew Chan and Myuran Sukumaran on Wednesday morning.

Australian photographer Adam Ferguson reacted with confusion when told by the gallery they would remove his portrait of Indonesia's president from public display.

The portrait was a finalist in the National Photographic Portrait Prize, and was set to be on display until June 8.

Ferguson, who shot the image as part of a cover shoot for Time magazine, said he would have preferred to see the work damaged than for it to be removed from the wall.

Speaking from Nepal, where he is covering the recent earthquake on assignment for Time, he said he had been contacted personally by gallery director Angus Trumble to inform him of the gallery's decision.

"Angus wrote to me and called me in Nepal and explained his position, which was kind of generous of him," he said.

He said while Mr Trumble had explained his concern that the work would be damaged, he thought the decision had been misguided.

"They don't actually own it, I own it. They haven't bought it off me, it's not like it's a high-value piece of work that they own," he said.

"He did mention that until yesterday they were determined not to take it down unless someone tried to deface it, which seems like a stupid thing because I don't think anyone in Australia would do that."

He said he would have preferred the image had stayed on the wall as a statement in itself, even if it were to be damaged.

"I think anybody that misconstrued the issues of national law in a sovereign country with a picture of the leader of that country has a totally misguided comprehension of the story and what's gone on. It seems to act in anger against the picture, it seems quite ridiculous," he said.

Mr Trumble told Fairfax Media he had taken the pre-emptive action to remove the portrait temporarily, in the wake of the news of and public reaction to the executions.

"My feeling yesterday [Wednesday] morning was that in view of the circumstances and our operations, and my best assessment of the risk of damage to the work of art, it was necessary to remove it from public display," he said.

"Also, I was swayed by the statements of both the Prime Minister and the Leader of the Opposition and of course the position of the Parliament  and the recall of our ambassador. So it's a temporary measure."

He said while there had not been any incident relating to the work and taking it down had been a preventive measure, he had a responsibility to protect all works in the gallery.

"My primary responsibility is the care of the works in our collection and the safety of our visitors," he said.