Tirso Alcantara was shot in the buttock by police last week who arrested him as he visited a house in the city of Lucena, military officials said at the time. But the alleged nature of the visit only came to light on Monday.
Alcantara, the married head of communist rebels in the region south of Manila, was tracked down because the military knew of his affair with a jailed comrade's wife, military spokesman Brigadier General Jose Mabanta said.
"He was arrested because he was visiting his lover," Mabanta told reporters.
"This means the members of the underground, just like any normal human beings, have their own share of personal problems."
Alcantara is now recuperating at a military hospital after surgery to remove a bullet embedded in his buttock.
Mabanta, who would not say if Alcantara was caught literally with his pants down, stressed it was up to the rebel's jailors to determine whether both his wife and mistress would be allowed to visit him in hospital.
Mabanta said Alcantara had been carrying out an affair with the wife of Eulogio Castillo, one of 43 suspected communist rebels who was arrested in a military raid in Morong, Rizal, in February last year.
The mistress is a former communist rebel who had quit the movement, Mabanta said.
President Benigno Aquino dropped the charges against the 43 and ordered their release last month as part of goodwill measures to help restart peace talks with the Maoist rebels, who have been waging a 41-year insurgency.
Mabanta described Alcantara as the top rebel in the provinces south of Manila.
"He is an experienced ideologue who has been in the movement since the 1970s," Mabanta said.
"He will be a big loss. He can be replaced but it will take time for his replacement, and even if they find a replacement it may not be his calibre."
The Communist Party of the Philippines and its 4,700-member New People's Army had demanded that the government free Alcantara before formal talks could resume in Norway next month.
However Mabanta said Alcantara would remain in detention and face charges in court unless the rebels could prove he was part of their peace-negotiating panel.