Nigerian President Umaru Musa Yar'Adua has ordered the retirement of 40 of the military's most senior commanders.
A military spokesman said there was nothing abnormal
They include the generals in charge of the army's five divisions.
Nigeria has been ruled by the military for 30 of the 47 years since independence but a coup is no longer likely, a BBC correspondent says.
Mr Yar'Adua was sworn in May - the first time one elected leader had handed power to another, although but the elections were widely condemned.
Former President Olusegun Obasanjo ordered a similar purge of the military shortly after his inauguration in 1999.
Mr Obasanjo, himself a beneficiary of a 1975 coup, said he wanted to rid Nigerian military of its penchant for plotting coups.
But the military says Mr Yar'Adua's motives for approving the retirement of 40 top army and air force commanders are different.
"We are now following due process and trying to go back to the best military traditions," Nigerian defence spokesman Col MD Yusuf told the BBC News website.
He also denied that any particular ethnic group was being targeted, which has led to unrest in the military in the past.
A spokesman for Mr Yar'Adua said the commanders were due to retire, having spent the required 35 years in service.
"No other motives should be ascribed to this purely routine movement of personnel in the armed forces," Olusegun Adeniyi said.
Mr Obasanjo became Nigeria's first democratically elected president after 16 years of military rule in 1999.