In an interview to BBC, which will be aired on Friday (14 October), Aisha said the government had been hijacked and alleged that her husband does not know most of the top officials he has appointed.
He made the comments to reporters in Germany, with Chancellor Angela Merkel standing by his side, who glared at him at first and then laughed.
But Buhari hit back, saying that having run for president three times and having succeeded at the fourth attempt, he could "claim superior knowledge over her and the rest of the opposition because at the end I have succeeded" in winning Nigeria's presidency.
President Muhammadu Buhari has said that his government will encourage more Nigerians to pay tax.
"The outbursts of the president's wife about his posture to governance is quite unfortunate and mismatch to the expectations of Nigerians and to worsen it, the response of President Buhari relegating his wife to his room and kitchen shows that Nigeria has been dragged to many centuries backward". Aisha Buhari said she may not support the president at the next election unless he got a grip on his government.
"Some of our leaders like the Senate President, Dr. Bukola Saraki, have made this same observation in the past and I think they meant well for the administration and the country. I will never do it again", Aisha Buhari said.
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Nigeria's President Muhammadu Buhari (2nd L) and his wife Aisha Buhari pose with Imo state governor Rochas Okorocha (L), Ogun State governor Ibikunle Amosu (2nd R) and Transport Minister Rotimi Amaechi during the president's birthday celebration in Abuja, Nigeria, in December 16, 2015.
Presidential spokesman Garba Shehu later took to Twitter to dismiss Buhari's comments as "banter".
"If it continues like this, I'm not going to be part of any [re-election] movement", she said to BBC.
"The President respects the place of women in our society and believes in the abilities of women. I will also join them in appealing to the president to do the needful", he said.
But as criticisms mounted, the presidency moved late Friday to downplay the president's remark, saying Buhari was only joking.