Morocco sent a second high-ranking emissary to Washington yesterday to assure the Reagan administration that there is "no substance" to the surprise unity agreement it signed with Libya last September that continues to provoke deep concern here.

Abdellatif Filali, who was named foreign minister just four days ago, met with President Reagan yesterday in the presence of national security affairs adviser Robert C. McFarlane for what the Moroccan side officially described as a "large exchange of views." During the brief meeting, he delivered a personal message from King Hassan II.

The White House had no comment on the meeting.

Filali also saw Vice President Bush, Secretary of State George P. Shultz, Deputy Secretary of State Kenneth W. Dam; he also met separately with McFarlane. A State Department official later described the meetings as "warm and friendly" and said the main purpose of Filali's visit was "to underscore there was no substance" to the Moroccan-Libyan merger and thus "no reason for American concern."

Despite these assurances, the official said, the unity pact is "still an issue" and Washington intends to continue monitoring developments for "potential problems" affecting the United States, "even cooperation between the Moroccan and Libyan airlines." The fear, he said, is that Libya may use such cooperation to infiltrate agents into Morocco or through it to other countries friendly to the United States, such as Egypt.

Last September, King Hassan sent a top adviser, Reda Guedira, here to allay fears over the pact.

One indication of the continuing malaise in U.S.-Moroccan relations over the merger is the king's not being scheduled to visit while one after another of the United States' other main Arab allies are. Algeria's leader, Benjadid Chadli, is making his first visit in April.

Algeria is Morocco's main rival for leadership in North Africa and the leading supporter now of the Polisario, the guerrilla movement for the independence of the Moroccan-occupied Western Sahara.

Since the pact was formally approved Sept. 1, little progress has been made toward any real merger of the two countries' institutions.

Earlier unity accords between Libya and other Arab countries have come to naught.

The king's decision to sign a unity pact with Libyan leader Col. Muammar Qaddafi, regarded here as a main backer of international terrorism, took the United States by surprise. Bush reportedly was particularly outraged by the action.

The king appeared to be acting on a gamble that he could end Qaddafi's support for the Polisario and thereby possibly keep the Organization of African Unity from recognizing it. Instead, in Addis Ababa, Ethiopia, in November, the organization formally seated the Polisario's Saharan Arab Democratic Republic.