Army chief Batista Tagme Na Waie said on state radio on Wednesday that Yalla, who was ousted in a 2003 coup, had seized the building early on Wednesday.
"This morning at dawn, Kumba Yalla and a group of men occupied the presidency of the republic. I call on the people to remain calm and stay at home because the situation will soon be resolved," Na Waie said.
About 50 soldiers were standing outside the building on Wednesday morning and witnesses said they appeared to be members of the presidential guard. There were more soldiers inside.
The head of presidential security told reporters outside the building that Yalla had already gone home, but that could not be immediately confirmed independently. There had been no shooting.
Yalla declared last week that he was still the legitimate ruler of the former Portuguese colony, raising fears of chaos ahead of presidential polls on 19 June.
Guinea-Bissau was originally due to hold elections this month to end a transition period meant to shepherd it back to democracy after the coup, but interim President Henrique Rosa pushed the date back.
Yalla's Social Renewal Party says the opposition never agreed to the extension, meaning Rosa and his government are no longer legitimately in power.
Many army generals in the impoverished country, racked by coups and civil war since independence in 1974, are from Yalla's Balante tribe and despite official declarations of support for the government, some are said to back the former leader.