Vice-President Yemi Osinbajo chaired the meeting instead of the 74-year-old Buhari, who has made few public appearances since he returned from medical treatment in London in early March.
The devout Muslim was also absent from Friday prayers last week and failed to attend his grandson's wedding on Saturday.
His spokesman said he had undergone "a long period of treatment" for an undisclosed illness in London earlier this year and needed rest. He was said to be working from his private residence.
Buhari worked from his office on Tuesday, he told reporters, adding: "Mr President will stick to his doctor's advice so that he can recover much more quickly."
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The head of state and his entourage have been under growing pressure to disclose his true health condition since he returned from the British capital after nearly two months away.
Prominent Nigerians and civil society activists have advised him to take medical leave.
Local media reported on Wednesday that former president Olusegun Obasanjo met other ex-military rulers Ibrahim Babangida and Abdulsalami Abubakar to discuss the situation.
But he rejected reports in recent days that the former army general was unable to eat or drink and was being fed intravenously.
"It's absolutely untrue that he's being fed," the minister said of the report on the online news site Sahara Reporters, calling Buhari's absence "not any strange development".
"It's exactly what he said, that he has been advised to take it easy by his doctor and that he will soon also go back (to London) for further treatment."
"He continues to carry out his responsibilities during this period," she wrote on her Twitter account on Tuesday evening.
The health of Nigeria's president has been a sensitive issue since the death in office in 2010 of Umaru Musa Yar'Adua, which sparked months of political turmoil and uncertainty.
During the 2015 election campaign, Buhari rejected opposition claims that he was seriously ill with prostate cancer and said they were a smear to show him as unfit for office.