As Egyptians on the bank waved and shouted "shalom," three Israeli warships sailed through the Suez Canal today in another application of the peace treaty between Egypt and Israel.

But despite this sign of normalization, it became apparent that the border between the two countries is not open, contrary to what was announced Sunday at a meeting between Prime Minister Menachem Begin of Israel and President Anwar Sadat of Egypt.

The three ships - 400-ton Israeli Navy landing craft identified as the Achziv, the Ashdod and the Ashkelon - passed through the 100-mile waterway at the head of the daily northbound convoy. They were the first Israeli military vessels to go through, and were on the way from Sharmel Sheik at the southern tip of the Sinai Peninsula to Israel's Mediterranean coast.

Reports from the scene said there were no Arab-flag ships in the convoy and that Egyptians in cities along the canal cheered in greeting and shouted "shalom," the Hebrew word for "peace," as the ships went by on their 14-hour journey.

Ordinary citizens of the two countries heard the announcement Sunday that the border was open and hoped to begin driving back and forth for business, shopping or sightseeing will have to wait, probably until next year.

Begin, after the meeting with Sadat and Secretary of State Cyrus Vance, had announced that "the borders of Egypt and Israel are open, that the citizens of Egypt will be able to visit Israel and those of Israel will be able to visit Egypt."

Skeptics here, including many Egyptians, thought there might be less to that announcement than met the eye. They apparently were right.

Egyptian officials led by Prime Minister Mustafa Khalil are now saying the border is open only to limited numbers of authorized persons on "specific business," and even those trips must wait until agreements have been worked out on technical details.

Reports in this morning's semiofficial press said a June 4 meeting between Israeli Foreign Minister Moshe Dayan and Egyptian officials will take up procedures for opening the border to individuals authorized to cross.

Khalil has told reporters that "this does not mean free movement" between the two countries and he has suggested that even the 5,000 residents of the El Arish area who formerly held jobs in Israeli-held territory or in Israel itself will not be permitted to cross.

There apparently are technical and political reasons why the border is not actually going to open to unrestricted travel. Egypt and Israel have no customs convention, no agreement on automobile papers or insurance, no consular agreements or visa arrangements and no currency exchange formula.

In addition, Egyptians say, it is unlikely that Sadat would want ordinary Egyptians, perhaps susceptible to Arab criticism of the peace treaty, making casual visits to East Jerusalem or to the occupied West Bank of the Jordan, where they might come in contact with viewpoints from which he has sought to screen them.

Sadat agreed when Begin was here in early April to open the border when El Arish returned to Egyptian control, as it was last Friday.

Last week, however, the Egyptians surprised and upset the Israelis by saying that agreement was only symbolic. Full freedom of movement, they said, would come only with full normalization of relations, and that would depend on progress in the negotiations on Palestinian autonomy that began last weekend.

Now, it appears that Sunday's agreement to go ahead with the opening was more a goodwill gesture to Begin than a concrete concession.

Under terms of the peace treaty, Egypt is not obliged to open the border right away, but the provision allowing Israel to send its ships through the canal is already in effect. The first civilian cargo vessel passed through a month ago.

The Associated Press reported:

Sadat said yesterday that foreign airlines can begin service between Tel Aviv and Cairo whenever they want to.

"There is no restriction, no boycott, let them come," he said of the foreign airlines. He was speaking with reporters during a trip through the canal aboard his presidential yacht.

Sadat added, however, that flights between the two countries by the Israeli and Egyptian airlines would begin only after Israel completes the initial phase of its withdrawal from the Sinai Peninsula at the end of the year. CAPTION: Picture, One of the three Israeli Navy ships that passed through the Suez Canal yesterday steams by an Israeli tank disabled in the 1973 war and left on the bank. AP