Lebanon's Christian Maronite militia, which has made no secret of the help it has received from Israel in its seven-year war with Palestinian forces, appears to be increasingly uncomfortable with the warm embrace that the Israeli invasion army is seeking to fasten around the Christian community here.

The unease was evident tonight in an unusual denial issued by Bashir Gemayel's Lebanese Forces, also called the Phalangists, that said the Maronite militia was not joining Israeli forces in the current fighting against the Palestinians. The Lebanese Forces "have not resorted, and will not resort, to a military initiative," the statement said.

Reliable eyewitnesses reported nonetheless that the Lebanese Forces had been involved in the battle around the state-run Lebanese University's science faculty today.

Close identification with the new Israeli occupation of Lebanon could have an effect on the future political role of the Maronites in this country of 16 officially recognized religious minorities. Many Maronites have openly voiced hopes that Israeli pressure would enable them to again dominate the country much as they did before the 1975-76 civil war.

But Gemayel, according to Lebanese politicians and foreign diplomats, has come to realize that he will face even fiercer opposition than before from Lebanon's Moslem majority, which has suffered a terrible toll in the current Israeli invasion. Increased Christian cooperation with the Israelis could only stiffen Moslem resistance to the Phalangists.

Looking down at Israeli armored vehicles stationed along the road from his mountain home today, a prosperous Christian businessman said warily, "Yes, we welcome them--if they do not stay too long."

Mindful of the Maronites' past reputation, Saeb Salam, a Sunni Moslem and former prime minister, said in an interview that he had told Gemayel, "If you want to finish Lebanon for good just cooperate with the Israelis."

And a Western diplomat who requested anonymity commented: "Any Maronite military role would be stupid if they want to come out on top in any national political settlement."

In the invasion's early stages the Lebanese Forces' officials insisted, as one said, "We are not suicidal--we are not going to be the infantry of the Israeli jets."

Yet the Israelis have sought to leave the impression that the Christians were actively supporting their forces. This was most pronounced Sunday night when an Israeli armored column reached territory controlled by the Christian militia. By the next day Israeli military spokesmen were saying that Lebanese Forces' scouts had guided their armor through the mountains and into Baabda, seat of Lebanon's presidency, which is traditionally reserved for a Maronite.

Today, an Israeli military spokesman again encouraged speculation that the Lebanese Forces were shelling and mortaring the science faculty. In the complicated politics of Lebanon, that charge could estrange the Shiite Moslems, the poorest and largest single community, whose children are dependent on that state-financed institution for their higher education.

Lebanese with a more Machiavellian view are openly wondering if the Israelis are not maneuvering to replace the Christians now that their common foes, the Syrians and Palestinians, are no longer major factors in Lebanon.

For the time being, signs of cooperation between the Christian forces and the Israelis abound. Israeli jeeps and other vehicles including tanks move freely through the Christian sector, clearly identifiable by the orange aircraft recognition panels they carry on their hoods.