Fouad Siniora, the Lebanese prime minister, said: "The government was not aware of and does not take responsibility for, nor endorses what happened on the international border."
The government said it was ready to negotiate through the United Nations to end the crisis.
Earlier, Ehud Olmert, the Israeli prime minister, said that he held the Lebanese government responsible for the two soldiers' safety. He called their abduction an act of war against Israel and said that the response would be "restrained, but very, very, very painful".
A source told AFP new agency that Lebanon had asked the United Nations to negotiate a ceasefire, but the request had so far been rejected by Israel.
He also said UN peacekeeping forces were on a "state of alert" along the border with Israel.
A Lebanese government source confirmed to AFP that Lebanon had requested a "total" ceasefire.
Lebanon's government includes two Hezbollah ministers.