The Israeli Army command said tonight that about 100 more Lebanese prisoners captured during Israeli raids into southern Lebanon earlier this year will be released Wednesday, leaving approximately 335, most of them Shiite Moslems, still held in Israel.

They will be the first to be released since 300 Arab prisoners were freed July 3. Israel insisted that move was not connected to any agreements with the United States or the Beirut hijackers of the Trans World Airlines jetliner, who had released the last 39 American hostages three days earlier.

On June 24, while the hijackers were holding the TWA hostages and demanding that Israel release all the Moslem prisoners, Israel freed 31 but said their release was related to an improving security situation in southern Lebanon and not to the hijackers' demands.

Since July 3, terrorist activity against Israeli and American targets abroad and against Israeli-supported security forces in southern Lebanon has increased, but Israeli officials continue to say they are not releasing prisoners in response to any pressure to fulfill promises that may have been made during negotiations for release of the TWA hostages.

Instead, they said, the Arabs had been held all along only as a temporary measure and would all be released as soon as security in southern Lebanon was stabilized.

A series of car bombings blamed on guerrillas of the Shiite militia, Amal, has been directed at members of the Israeli-sponsored South Lebanon Army in the narrow security zone established north of the border by Israel after it announced the withdrawal of its forces from Lebanon.

An Israeli military spokesman said today that an Israeli soldier was slighly wounded yesterday when a land mine exploded under his vehicle in the security zone.

Israeli troops have regularly sent patrols into the security zone in search of guerrillas, according to the Army command. The car bombings prompted Israeli air and ground raids against alleged guerrilla bases in Lebanon. In Copenhagen yesterday, a U.S. business office and Jewish centers were damaged by bombs that a caller linked to the Israeli raids.

The pace of the release of the Lebanese prisoners -- who the United Nations and United States have said were transferred to Israel in violation of international law, a charge Israel rejects -- was criticized in Beirut today by Shiite Moslem militia leader Nabih Berri.

Berri, who played a key role in gaining the release of the TWA hostages, met with U.N. envoy Jean-Claude Aime to complain about what Berri called the "Israeli conduct and crimes in Lebanese villages" and to express his "strong displeasure with the American role regarding promises made by President Reagan" during the TWA hijacking "for the release of all prisoners, which has yet to take place," special correspondent Nora Boustany reported from Beirut.

The announcement of the planned prisoner release came as the Army command in Tel Aviv said that Israeli gunboats off the coast of Sidon, a port city in southern Lebanon, exchanged fire with shore gunners today after intercepting what a military spokesman called a "suspicious" merchant vessel.

The command said Navy gunboats on "routine patrol" off Lebanon attempted to approach the cargo vessel and were fired upon by the ship and shore positions. One Israeli crewman was slightly wounded, officials said, and the freighter was set on fire.

Several times in recent months, Israeli ships have stopped and fired upon vessels off Lebanon that have been described by military authorities as "suspicious."

Witnesses in Sidon today told reporters in Beirut that the Israeli gunboats also shelled the port and the Moslem-held hills nearby, wounding six civilians and three crewmen of the intercepted ship. The Israeli spokesman denied that the gunboats had fired on Sidon.

According to the accounts from Sidon, four Israeli warships were about two miles off the Lebanese coast when they shelled the harbor. Moslem militiamen entrenched in hilltop positions used artillery in an attempt to drive away the gunboats but missed them.

Michael Kinghares, the Greek captain of the Lebanese-owned cargo ship, said he had been intercepted by Israeli gunboats three days ago as he tried to unload a cargo of Romanian cement at Khaldah, a newly constructed dock under Druze control south of Beirut. He said the Israeli ships machine-gunned his vessel, damaging it slightly, after he ignored orders to sail to the Israeli port of Haifa.

"I asked the Israelis' permission to sail to Tyre, but they refused," he told reporters. "This morning, I tried to reach Sidon by sailing close to the shore, but the gunboat intercepted us again and instructed me to accompany it to Haifa. I refused and instead entered the port and the Israeli gunboat opened fire."

Israel's insistence on halting the cargo ship was seen in Lebanon as an indication that it is responding to reports that guns are being shipped into the Palestinian refugee camps at the edge of Sidon.

Security and relief sources in Lebanon have reported the arrival in Sidon of arms for Palestine Liberation Organization Chairman Yasser Arafat's loyalists. Sunni and Shiite Moslem politicians have warned that the PLO forces are preparing for another round of fighting with local militias.