"A short while ago, Israel navy soldiers boarded the vessels which were en route to the Gaza Strip, attempting to break the maritime security blockade that is in place in accordance with international law," it said.
An Israeli security source told AFP were no injuries during the boarding operation.
The 15 activists aboard the Irish Saoirse (Gaelic for Freedom) and the 12 aboard the Canadian Tahrir (Arabic for Liberation), who had set sail from Turkey on Wednesday, were being towed to Ashdod port in southern Israel, it said.
On arrival, those on board would be transferred to the custody of the police and immigration authorities in the interior ministry, the army said. Five of those on board the Tahrir are journalists, organisers said.
"The Israel navy soldiers operated as planned, and took every precaution necessary to ensure the safety of the activists on board the vessels as well as themselves," the statement said.
Activists had organised a major attempt to break the Israeli blockade in May 2010, when six ships led by the Turkish Mavi Marmara tried to reach Gaza.
Israeli troops stormed the Marmara, killing nine Turkish activists and sparked a diplomatic crisis with Ankara, which expelled the Israeli ambassador and has cut military ties with the Jewish state.
Earlier this year, a second flotilla tried to reach Gaza, but several ships were sabotaged -- which activists blamed on Israel. Only the French-flagged yacht, the Dignity, was able to attempt the last leg of the journey but was stopped by the navy and those on board were deported.
Israel says its blockade is necessary to prevent weapons from entering the coastal territory, which is run by the Islamist Hamas movement.
Two months ago, a UN report on the flotilla raid accused the Jewish state of acting with "excessive force" but found that its naval blockade on the coastal territory was legal.