The United States and Cuba ended almost 17 years of diplomatic isolation from each other yesterday by opening "interests sections" to represent the two countries in Washington and Havana.

Although the move does not mean a restoration of full diplomatic relations, it marks the most signficant step so far in a slowly evolving rapprochement between the longtime hemispheric antagonists.

That progress was noted by Philip C. Habib, under secretary of state for political affairs, who called this latest move "a beginning, not an end. It is not a big step, but it is a significant one just the same."

Habib's speech at a ceremony in the Czechoslovakian embassy, which has represented Cuban interest shere, reflected the festive, upbeat atmosphere by welcoming the opportunity for a renewed dialogue where "we can speak to each other directly."

But Habib carefully added a cautionary note: "The dialogue wont always be an easy one."

His words were echoed in Havana by acting Cuban Foreign Minister Peligrin Torras, who told a gathering that "for the goal of re-establishing normal relations, a long and difficult road still lies ahead."

The difficulties in moving onto that road were perhaps best symbolized by the physical conditions that greeted the two missions on their arrival in the two capitals. The Cuban group will be forced to work out of the Czechoslovakian embassy for an indefinite period because their long-closed and neglected Cuban embassy here is badly in need of repair and remodeling.

Similarly, when the U.S. mission to Havana opened the doors tof the U.S. embassy there earlier this week, they found what one official described as a "time capsule."

Among the relics encountered by their cleanup crews were portraits of Dwight D. Eisenhower, the President who broke relations with Havana, and Philip Bonsal, the last U.S. ambassadar there. They also found a coke machine whose age was betrayed by the fact that it required only a nickel for a bottle, and films of the University of Washington beating the University of Minnesota 17-7 in the 1961 Rose Bowl game.

The speeches in both Washington and Havana underscored the facts that some thorny, unresolved conflicts still divide Washington and Havana and that considerable negotiation and compromise is required by both sides before they can be cleared out of the way.

In diplomatic circles, the expectation is that is will be several months, at the very least, before any significant progress is made. For one thing, State Department sources say, the Carter administration has decided to put relations with Cuba on the back burner until the battle for congressional approval of the Panama Canal treaties is concluded.

Technically, the eight-member Cuban mission here is part of the Czechoslovakian embassy. Similarly, the 10 person delegation of diplomats sent by Washington to Havana is supposed to operate as a section of the Swiss embassy there.

But, while they will not fly their national flags, the two missions will function, for all practical purposes, as embassies able to deal directly with the governments in the two capitals.

Such direct dealings have not taken place since January, 1961, when the United States, alarmed at Fidel Castro's rise to power and his subsequent installation of a Communist regime in Cuba, severed relations with Hanava.

The years immediately afterward were marked by deep animosities, fueled on one side by Cuba's attempts to export Communist guerrilla movements to other Latin American countries and on the other by Washington's attempts to quarantine the Castro government through economic boycotts and the suspension of Cuba from the Organization of American States.

At times, these tensions flared into global crises - most notably in 1961 when the United States supported the obortive Bay of Pigs invasion by anti-Castro Cuban exiles and in 1962 when the emplacement of Soviet offensive missiles in Cuba precipitated a U.S.-Soviet confrontation.

In recent years, as Cuba has retreated from its policy of trying to foster Communist revolution in other Latin countries, the two governments have made several false starts toward improved relations. Nothing came of these initiatives, though, until President Carter took office and launched a drive for improved ties.

Of the problems that await resolution, Ramon Sanchez-Parodi, who will head the Cuban interests section here, said yesterday that his government regards the ending of the U.S. economic and trade blockade as a necessary precondition for restoring full diplomatic relations. He also warned that Washington will have to clamp down on "the aggressive actions" carried out by Cuban exiles "against Cuba from the United States territory."