It was the first such arrest raid in the territory since Israel pulled out of the territory a year ago
Ali Muamar, a Palestinian known to residents as a Hamas loyalist, said he was asleep on a bed outside his home near the Rafah refugee camp in south Gaza when he woke up and saw uniformed Israeli soldiers scaling down the walls of his courtyard with ladders.
"They attacked me all of a sudden," he said. "They blindfolded and handcuffed me and started beating me up with the butts of their rifles and kicking me with their boots."
Muamar said the soldiers raided his home, took his computer and left after less than an hour with his sons - Osama, a doctor who had arrived in Gaza last month from Sudan, and Mustafa, a student of Islamic law.
A spokesman for Hamas, which won control of the Palestinian government in a parliamentary election in January, denied the men detained were connected to the group.
An army spokeswoman confirmed troops had entered Gaza and detained the men, saying they were Hamas fighters who had planned to carry out an anti-Israeli attack. Muamar said he and his sons were not involved in hostilities against Israel.
Israel pulled troops and Jewish settlers out of the Gaza Strip last summer after 38 years of military rule.
Troops had entered the area several times in recent weeks in an effort to stop Palestinians from firing rockets into the Jewish state but had not carried out arrest raids.
Israel has increased its air strikes in Gaza in parallel to a surge of rocket attacks and has killed more than two dozen Palestinians, including fighters and civilians, in missile strikes since the beginning of June.
Top Israeli security officials recently had hinted they would not rule out ground raids into the territory should rocket attacks by Palestinian fighters in Gaza continue.