Bolivia's first election in 12 years, held Sunday, has run into problems.

The tortuously slow counting of ballots - coupled with charges of widespread fraud confirmed in part yesterday by a team of international observers - has created a climate of suspicion and uncertainty here. There is an increasing expectation that only violence will in the end decide who will emerge as Bolivia's next president.

The situation has been exacerbated by harsh and provocative statements made over the past 24 hours by Hernan Siles Zuazo, the leading center-left candidate, and Juan Pereda Asbun, the military government's choice to succeed retiring President Hugo Banzer.

Pereda was the favored candidate in the election and was leading his opponents yesterday with more than 45 percent of the vote. A third of the ballots have been counted. But Pereda was not getting a majority of the votes, even based on returns that his opponents said were being fixed in Pereda's favor.

The election may place the Carter administration in a difficult position because U.S. diplomats here and in Washington have strongly supported Bolivia's return to democracy after more than 14 years of military rule.

Bolivia was to have been a model for other Latin military governments that have resisted turning over power to democratically elected civilians.

Now, with the election here being challenged as fraudulent and with the opposition parties looking to the Carter administration for support, the State Department and the White House will be under pressure to sort out what is happening and respond in some way.

The Banzer government has closed Bolivia's universities for an indefinite period and has warned that it will not tolerate "chaos and anarchy."

There are increasing rumors here that the military will not allow Siles and two other candidates to form a government even if they receive a majority of the seats in a newly elected parliament, which will decide who is president if no candidate receives more than half of Sunday's vote.

Siles has called publicly for "popular resistance" to what he said was a government effort to steal the election from him. Victor Paz Estenssoro, a former president who is considered a centrist, and Rene Bernal, the Christian Democratic candidate, also is a centrist.

Seven candidates ran in Sunday's election. Based on official returns available yesterday afternoon, Pereda had 46.8 percent of the votes counted; Siles had 17.1 percent; Bernal had 16.3 percent and Paz Estenssoro had 13.6 percent.

Siles' percentage was expected to jump sharply as the La Paz vote, inexplicably helf up, is included in the totals.

A group of international observers, led by Lord Erik Avebury of Britain, said they saw clear and numerous irregularities Sunday during the election, but it will be almost impossible to determine to what extent these irregularities affected the size of Pereda's vote.

The charges and countercharges, begun Monday morning by Siles and carried on later in the day by Pereda, appeared designed to prepare Bolivians for a confrontation over the results.

Siles said Monday that it was clear to him that the only way Pereda could get a majority was for the government to fix the vote counting.

Siles insisted that he, Paz Estenssoro and Bernal had won a majority and he likened the situation to 1952 when Siles led an armed insurrection that defeated the military, which had carried out a coup, rather than allow Siles and Paz Estenssoro to assume office after they had won an election.

Later Monday, Pereda accused Siles of being an agent of international communism. "We will defend ourselves," Pereda said.

Meanwhile, the international observers invited here by the Permanent Assembly for Human Rights returned to La Paz yesterday from the nine areas of Bolivia where they spent election day and said many polling booths had no opposition party ballots, that soldiers intimidated voters and that opposition party members were prohibited from observing vote counts at some polling places.