Israeli state prosecutors indicted the men in the Israeli city of Nazareth on Tuesday.
According to Israeli justice ministry officials, the men were captured during an army offensive in southern Lebanon after Hezbollah seized two Israeli soldiers on July 12.
Mahmud Ali Sulaiman, Muhammad Sarur, and Mahir Qurani, appeared before a civil court in the northern Israeli town of Nazareth and will not face a military tribunal.
Using the criminal trial is seen as part of Israel's refusal to recognise Hezbollah as a legitimate fighting force.
Micky Rosenfeld, a police spokeman, said the men were accused of having trained in Iran, and Sulaiman was charged with taking part in the cross-border attack.
Israel is believed to have detained about a dozen Hezbollah fighters during the month-long war.
Convictions could complicate any future swap deal for the two Israeli army reservists who are still being held captive in Lebanon.
An internal inquiry by the Israeli army has found that Military Intelligence knew that Hezbollah was planning to capture Israeli solders shortly before July 12, according to the Israeli newspaper Haaretz.
Israeli soldiers have complained
of poor planning and tactics
The information, if properly handled, could have prevented the capture of Eldad Regev and Ehud Goldwasser, but was not analysed and passed on to troops in time, the inquiry concluded.
The Israeli army refused to confirm or deny the report, saying the issue was still being investigated.
Israel's cabinet has appointed a commission to investigate the way the government and the military handled the Lebanon war, but rejected calls for an independent inquiry.
Ehud Olmert, the prime minister, has been criticised for what is seen by some as an ill-prepared campaign in Lebanon that failed to crush Hezbollah.
Israeli reservists who fought in Lebanon have complained of poor planning and tactics.
Thousands of Israelis have joined protests to demand an independent inquiry into the war by a so-called state commission whose members would be appointed by a supreme court judge.
Olmert has said such an investigation would be too time-consuming and instead Eliayhu Winograd, a retired judge, and four other people will examine how political leaders and military commanders conducted the war.
Outside the prime minister's office, dozens of veterans held a demonstration calling on Olmert, Amir Peretz, the defence minister, and Lieutenant-General Dan Halutz, the military chief of staff, to resign.
Israeli media said the panel would begin work on Monday.