Special Mideast emissary Philip C. Habib reported to President Reagan yesterday on his latest mission to reinforce the "fragile" cease-fire between Israel and the Palestinians as the State Department clarified its application to Jordanian and Syrian borders.

Speaking to reporters after a meeting with Reagan, the veteran diplomat declared that "all parties realize more than ever the grave implications of a major breakdown of the cease-fire" that he negotiated in the area last July. He went on to say that the situation is still "fragile.".

Habib, in response to questions, said Israeli officials gave him "a clear indication that they wish to abide by the cease-fire." He understands, he said, that they will "not be the first to attack."

The Israeli government, increasingly edgy about a buildup of military equipment in the hands of Palestinian forces in southern Lebanon, has put the United States on notice that it reserves the right to shatter the truce in case of "clear provocation."

That term has not been defined with precision, but yesterday the State Department made clear that some attacks into Israel through Jordan or Syria would be regarded by Washington as cease-fire violations.

The incursion by six Palestinian commandos who entered Israel through Jordan Jan. 30 prompted Israeli Defense Minister Ariel Sharon to recommend that his forces be unleashed to strike Palestinian troop concentrations in southern Lebanon in retaliation. At that time, Prime Minister Menachem Begin turned down Sharon's attack plan but dispatched the chief of army intelligence, Maj. Gen. Yehoshua Saguy, to voice urgent concern to Washington and to serve notice that strikes through Jordan along with other "provocations" could shatter the cease-fire.

The U.S. position on the application of the cease-fire to Palestinian military actions through Jordan or Syria was unclear at that time, according to Israeli sources.

The State Department statement yesterday, evidently drawn up by Habib on the basis of his latest round of discussions in the area, said that "any hostile action originating from Lebanon but going through Syria and Jordan into Israel would be a violation" of the U.S.-sponsored cease-fire.

At the White House, Habib called the statement "nothing extraordinary" and said it reflected what had always been his clear understanding. Such an understanding had not been clearly expressed in earlier U.S. pronouncements, however.

Regarding the continued presence of Syrian anti-aircraft missiles in Lebanon's Bakaa valley, Habib said that they are "still a problem" but that discussions on this subject had been overshadowed during his latest trip by tension over other aspects of the situation.

Israel's threat to take military action against the missiles last spring generated fears of a dangerous conflagration, and prompted Reagan to call Habib from retirement to become special U.S. emissary in the area.

After two months of nearly constant shuttling, Habib announced a cease-fire involving Israel and the Palestinian forces in southern Lebanon July 24. He was unable to arrange for the withdrawal of the Syrian missiles, however.

In response to various incidents and concerns, Habib returned to the area for several weeks last November and December. His latest trip, which began three weeks ago, was prompted by growing fears of an Israeli invasion after Sharon's recommendation early last month.

Habib said yesterday he is returning to his retirement home in California but "I'm at the president's disposal at any time" if further peace efforts are required.