Nearly two weeks after replacing ousted right-wing president Carlos Humberto Romero, El Salvador's new civilian-military junta faces many of the same problems, and lack of solutions, that contributed to Romero's downfall.

Despite initial pledges to free nearly 300 political prisoners allegedly detained by the Romero government in secret jails, the junta now says it cannot find any such prisoners.

No one -- except Romero -- denies the prisoners existed. Junta sources said that, following an investigation, the new government believes they are all dead. But human rights activists have rejected that explanation and charged the junta with operating the same coverup as Romero.

At the same time, there have been widespread demands for punishment of officials involved in the arrests, alleged torture and presumed murder of prisoners. So far, the junta has made no charges and no arrests in the cases.

The junta has promised to dismantle or reorganize the official security organizations and wage war against rightist paramilitary groups. So far, however, it has been unable or unwilling to do anything except change a few high-level commanders and condemn continuing official and unofficial violence against alleged subversives.

Long in the planning stages, the Oct. 15 coup by military moderates came about with the blessing of the United States, which feared that growing political polarization and violence might result in a radical government installed by force.

Although the Carter administration has decided to support the new Sandinista government that overthrew Anastasio Somoza in nearby Nicaragua, and had begun to disassociate itself with Romero's repression, it has little desire to see a second leftist government in Central America.

Amid a feeling that little time remains to defuse El Salvador's political powder keg, the junta so far has failed not only to keep the extreme right in line, but its efforts to woo the radical left have met with little success.

Although two of El Salvador's six principal leftist groups, ranging from Marxist guerrillas to militant student-labor-peasant coalitions, initially responded to promised junta reforms by calling a temporary suspension of violence and provocation, all have now denounced the new government and resumed their activities with a vengeance.

Last Monday, in a repeat of a familiar pattern under Romero, a march organized by the United Popular Action Front was broken up by gunfire and at least two youths were killed. The junta had issued strict orders for police to stay away from the demonstration, but the initial shots that brought return fire from leftists carrying concealed sidearms reportedly came from rightist provocateurs dressed in civilian clothes.

Although the government condemned the violence and denies responsibility, the fuel was added to the leftist fire.

By midweek, leftist groups had occupied churches and two government ministries, again a traditional tactic, and dared the junta to meet their demands or try to oust them.

As repression increased under Romero, the left had thought itself close to the desired "popular insurrection" in which the economically and politically oppressed Salvadorian masses would rise up in arms and install a socialist government.

Many of El Salvador's lower economic groups had begun to listen. But the promised junta reforms at least temporarily took away some of the leftist steam.

The militant left now appears confused and desperately trying to convince the masses that the new government, despite its liberal facade, is the same as the old.

The left also has begun to turn against former moderate allies with which it had tentatively joined against Romero. Two of the militant coalitions who were represented in a center-left political forum organized last summer against the old government have now withdrawn.

The forum was initially organized in part by the Christian Democratic Party, traditionally El Salvador's largest moderate opposition group. The Christian Democrats have accepted several Cabinet posts within the new government, and the left charges they have been co-opted.

In the most striking incident of what is rapidly becoming a reorganization of sides in a continuing political battle, the militant leftists on Thursday organized an attack against Christian Democratic leader Jose Napoleon Duarte on his return from seven years in political exile.

When Duarte left El Salvador in 1972 for Costa Rica and later Venezuela, he was probably the most popular political figure in the country. When he flew into San Salvador's international airport Thursday, an estimated $100,000 people turned out to welcome him.

Both the crowds and Duarte, however, were pelted with rocks and eggs by angry leftists. Along the path of the procession hung banners denouncing both Duarte and Archbishop Oscar A. Romero -- a human rights activist and critic of the previous government who has expressed cautious optimism over the junta -- as "pro-imperialist traitors."

A downtown rally for Duarte erupted into an all-out brawl, including widespread looting and fires, when leftist demonstrators tried to outshout the Christian Democrats. Youths circulated in the crowd carrying weapons and numerous threats were reported against Duarte's life.

Neither the government, which feared new charges of repression, nor the Christian Democrats, who fear new charges of association with the government, felt secure politically in organizing protection of Duarte's life. g