However, government spokeswoman Patricia Kaliati said she was unable to confirm the president had been taken to hospital.
Medical sources told Reuters they were preparing to airlift Mutharika to South Africa as soon as he stabilised.
"He was brought in on a convoy of three cars. His head was covered to hide his face as he was wheeled in on a wheel chair," said one hospital source.
Asked whether Mutharika had been taken into hospital, Kaliati said: "What you are saying is news to me. I was with him this morning and I can tell you that he is alright."
Mutharika, 78, has been president of the landlocked southern African nation since 2004 and presided over more than five years of economic boom, during which Malawi became one of the world's fastest-growing countries.
The growth came to a halt last year after a dispute with Britain led to tit-for-tat diplomatic expulsions and a freezing of millions of dollars of aid.
The move by Malawi's biggest donor exacerbated an already acute dollar shortage, hampering imports of fuel, food and medicines, and leading to a depreciation in the value of the local currency kwacha.
Mutharika's diplomatic isolation and economic plight worsened in July 2011 when police killed 20 people in a crackdown on a wave of protests against the government.
In response, the United States shelved a $350 million programme to overhaul the dilapidated power grid.
News of Mutharika's hospitalisation spread quickly on the social media sites Twitter and Facebook, with many speculating about his health and what may come next.