They also questioned delays in releasing the results of the presidential contest in Zimbabwe's first election since Robert Mugabe was forced to resign following a de facto coup in November after almost 40 years in power.
The ruling party's margin of victory in legislative elections makes Mnangagwa the stand-out favourite in that race, which featured 22 candidates.
"The electoral commission failed to meet the mark in a number of ways and the election failed to meet the mark in a number of ways", said Johnnie Carson, a former US assistant Secretary of State for Africa, who is part of an observer mission from the International Republican Institute and the National Democratic Institute.
Zimbabwe's long-ruling Zanu-PF party won a parliamentary majority in the country's election, causing opposition supporters to take to the streets alleging rigging.
The Zimbabwe Republic Police (ZRP) said the army had to intervene to help disperse MDC Alliance supporters because it did not have the capacity to deal with the crowd.
The campaigning, Mnangagwa said, and the voting process had been peaceful and as such, "incidents of wanton violence and hooliganism which broke out this afternoon in the capital, come as a complete surprise".
"The longer it lasts.the more a lack of credibility will arise in Zimbabwe", said Elmar Brok, a European Union lawmaker who heads the bloc's observer mission.
Mnangagwa, a former deputy president who fell out with Mugabe and then took over from him, has said his showing in the presidential polls was "extremely positive" while urging people to wait for official results. "The strategy is meant to prepare Zim mentally to accept fake presidential results", he tweeted.
The commission said it would release vote totals "sometime" on Thursday, even though it said most of the results "are here with us". Mugabe was later be deposed as leader of ZANU PF and replaced with Emmerson Mnangagwa.
The violence started soon after opposition Movement for Democratic Change (MDC) leader Nelson Chamisa claimed he had won the popular vote.
Scores of his supporters who had been burning tyres in the streets attacked riot police near the electoral commission headquarters.
But, is there a possibility that the opposition MDC-Alliance which has lost most of the Parliamentary seats to win the Presidential contest?
This is the first time ever that security forces have shot and killed civilians while election results are still being released by the electoral body.
"These matters have been referred to the attention of the police for investigations as to whether or not the Electoral Act and or the electoral conduct may have been violated". The 40-year-old vibrant leader says they have "won the popular vote".
Chamisa has said he is confident of victory, and has threatened in the lead-up to the polls he will not to accept a Zanu-PF victory.
Voters traditionally pick a presidential candidate based on their party affiliation and the trend in the parliamentary election was expected to continue when results for the president are announced this week.
The MDC also questioned the pace of releasing results from the presidential vote.
Zimbabwe was once one of Africa's most promising economies but under Mugabe's rule became tainted by corruption, mismanagement and diplomatic isolation.