Relatives of the three boys said they were released early Thursday after being seized by Israeli forces on Wednesday night while they were playing.
Palestinian sources had said the boys were taken away, bound and blindfolded from their home village of Aurif near the Palestinian city of Nablus during the night.
Two of them are aged 10 and the other one 11.
"They are under investigation for actions hostile to Israeli military forces," said an Israeli military source, who declined to give further details.
Israel has regularly detained children for alleged roles in the uprising, which erupted in September 2000.
Palestinian resistance groups which have been spearheading the uprising reaffirmed their commitment to a ceasefire they declared late last month.
Hamas said on Wednesday the truce was in jeopardy due to Israel's refural to release thousands of Palestinian prisoners as part of the agreement.
Officials from four groups, including Hamas pledged their commitment to the ceasefire during a meeting with an Egyptian security delegation in Gaza on Thursday.
But they made clear to the Egyptian envoys that "the prisoner issue could blow up everything", officials from the groups said.
US backs Abbas
Washington has thrown its support
Meanwhile, the United States will give the Palestinian Authority $20 million in an effort to shore up support for Palestinian Prime Minister Mahmoud Abbas.
The White House said on Wednesday the funds would be used for "humanitarian purposes" and kick-start the beleaguered Palestinian economy.
Since the start of the Palestinian intifada or uprising against Israel’s occupation, Israel has imposed crippling blockade over the West Bank and Gaza Strip and denied hundreds of thousands of Palestinians from reaching their jobs.
The move represents the Bush administration’s deepening commitment to Abbas after shunning Palestinian President Yasser Arafat.
“We believe it’s important to act now to reinforce the positive progress, to signal support for Prime Minister Abbas, for Finance Minister (Salam) Fayad, to help establish authority on the ground,” said State Department spokesman Phil Reeker.
The White House said the Palestinian package of $20 million had received “considerable support in Congress”.
This year Congress approved $2.76 billion in its annual package to Israel. In addition to nearly $3 billion in direct aid, Israel also receives around $3 billion in indirect aid.