The 58-year-old leader has not been seen in public since being flown back after three months of treatment in Jeddah for a heart condition. There have been no announcements on his health but presidency sources say he remains in intensive care.
His return while still too frail to govern raised fears that his inner circle of aides, led by his wife Turai, would fight to maintain their influence over Africa's most populous nation and seek to undermine Acting President Goodluck Jonathan.
A power struggle at the top of the OPEC member nation of 140 million people could bring paralysis in government decision-making, threatening an amnesty programme in the oil-producing Niger Delta and stalling momentum on reforms.
Several hundred people, many wearing T-shirts with "Save Nigeria Group" on the front and "Enough is Enough" on the back, gathered near to a city centre hotel under the watch of police officers lining the avenue.
"We want the invisible president to be revoked. We are tired of a president we can't see, who can't govern. We want to see him," Babatunde Ogala, a politician from the commercial capital Lagos, told the gathering crowd.
"If we can't see him we want someone else who is allowed to govern. Why is a cabal controlling our country," he said.
Officials organising the march said they planned to walk to Aso Rock, the presidential villa, and hand a letter of protest to the Secretary to the Government of the Federation, who co-ordinates between the presidency and government ministries.
"Turai, leave Nigeria alone" and "Jonathan get decisive now" were among the banners held up above the crowd.
A police spokesman addressed the protesters, pledging that the security forces were there to protect them and would help them carry their message "in a peaceful manner". He said officers were not carrying tear gas or weapons.
Such political demonstrations are relatively rare in Nigeria, where the vast majority of people get by on $2 a day or less and feel politics is a game played by multi-millionaires whose outcome has little effect on their daily lives.
Similar marches in recent months have passed peacefully.
Should Yar'Adua be formally declared too sick to govern, or resign or die, Jonathan would be sworn in as head of state and complete the unexpired presidential term, which runs to May next year, with a new vice president.
The demonstrators are also demanding electoral reforms to avoid the sort of chaos seen in the 2007 polls which brought Yar'Adua to power, a vote so marred by ballot-stuffing and intimidation that observers said it was not credible.