Parliament last month passed legal changes that allow civilian courts to try military personnel during peacetime and bar military courts from prosecuting civilians.
The changes comply with the European Union's requirement that the authority of army courts be restricted to military affairs, Gül said in a statement on his website.
"In implementing these reforms, it would be beneficial for legal changes to be made to remove doubts likely to arise over discipline and legal guarantees from the perspective of military service," he said.
Turkish media last week cited senior military officials as saying the law was unconstitutional and that it threatened to create clashes between the military and civilian judiciary.
Prime Minister Recep Tayyip Erdogan's ruling AK Party, which has its roots in political Islam, has been at odds with the army and the rest of the secularist establishment over government policies and the direction of the predominantly Muslim country.
Turkey's military, which has forced four governments from power since 1960, considers itself the guardian of the country's secular constitution. But it has seen its influence in public life diminish as Ankara pushes EU-inspired reforms.
Deputy Prime Minister Cemil Cicek, who is also the government's spokesman, said the law was a "step to improve democracy" in EU-aspirant Turkey.
Cicek said Gül had recommended the government make some amendments to allay concerns by the military, including legal assurances regarding the duties of military personnel.
There was no immediate reaction from the military.
The legislation allows civilian courts to try members of the armed forces who are accused of crimes including threats to national security, constitutional violations, organising armed groups and attempts to topple the government.
The main opposition Republican People's Party (CHP), which has aligned itself with the military, will appeal to the Constitutional Court to strike down the measure, Mustafa Ozyurek, a CHP deputy, told NTV news channel.
(EurActiv with Reuters.)
