She complained that her 59-year-old husband had been "dragged out and treated like an animal" by the soldiers.
"I don't know his condition. He needs regular medication," she said.
General Fonseka was defeated by incumbent Mahinda Rajapaksa in last month's poll
"We always knew that the government will try to arrest my husband, but we never thought they would do it in such a disgusting manner."
The government says Fonseka, who as the senior general helped defeat the Tamil Tiger rebels last May, will be court-martialled for allegedly planning to overthrow the government while serving as the head of the army.
Major-General Prasad Samarasinghe, a military spokesman, denied that Fonseka is cut off from family or friends.
"Family members are allowed to see him and he has been allowed to obtain legal advice also," he told the Associated Press news agency.
Rauf Hakeen, an opposition politician who was with Fonseka when he was taken into custody, said the military action was "undignified" and he felt ashamed.
"The way the troops spoke to General Fonseka and the way they forcibly dragged him away is a disgrace to the security forces," Hakeem told the AFP news agency.
"It is a shameful way to treat your former commander."
In an official statement, the government said that the former army chief was "hell-bent" on betraying the country's "gallant armed forces".
It cited as evidence the general's remarks on Monday that he would be ready to give evidence in an international court on war crimes charges against the state.
More than 7,000 civilians were killed in the final months of the fighting that crushed the rebels last May.
Human rights groups have accused the military of shelling hospitals and heavily populated civilian areas during the fighting, and the rebels of holding the local population as human shields.
A US state department report has accused both sides of possible war crimes, and the issue remains a sensitive subject for the government.
Many credit Fonseka with winning the war against the separatist Liberation Tigers of Tamil Eelam (LTTE), but he fell out with Mahinda Rajapaksa, the country's president, soon after and the pair fought a bitter election campaign. Parliament dissolved
Fonseka was defeated by Rajapaksa last month by six million votes to four million.
Fonseka has accused the government of rigging the election and has vowed to challenge the result in the Supreme Court. He has just one more week to file the relevant legal papers.
The former army chief has also accused the government of trying to frame him and alleges there is a plot to kill him.
Meanwhile, Rajapaksa has ordered the dissolution of parliament with effect from Wednesday, clearing the way for early elections.
Official sources said elections for a new parliament will probably be held on April 8.