Hundreds of opposition activists in Zimbabwe are in hiding from an army-led crackdown days after ruling party leader Emmerson Mnangagwa was the presidential winner of a hotly contested and controversial election.

Soldiers moved through suburbs of Harare, the capital, and satellite cities on Friday night and early on Saturday morning, beating supporters of the opposition Movement for Democratic Change (MDC), firing weapons outside the homes of its MPs and sealing off the homes of leaders’ families.

Activists reported dozens of injuries – including broken legs and arms – but said that many people were too scared to seek medical attention for fear of being identified and detained. “There are a lot of people hiding as soldiers are going door to door. There are people disappearing. We don’t know how many – maybe 30, maybe 50. They are clearly trying to scatter the leadership, to stop us organising,” Nkululeko Sibanda, an MDC spokesman, said.

On Monday, millions voted in the first election since Robert Mugabe, now 94, was ousted last November after 37 years in power. The rise in violence since has come as a huge disappointment to those who hoped the brutality associated with Mugabe’s rule would disappear with .

Mnangagwa, a 75-year-old former spy chief and Zanu-PF party stalwart, won with 50.8% of the vote, narrowly avoiding a run-off with the 40-year-old MDC leader, Nelson Chamisa.

Chamisa, a former pastor and lawyer, who won 44.3% of the vote, according to election officials, has called the polls “fraudulent and illegitimate”.

Election day was peaceful, but six people were shot dead two days later when soldiers opened fire on MDC protesters in the centre of Harare. On Thursday, 18 were arrested at the opposition party’s headquarters by police on suspicion of incitement or organisation of political violence. On Friday, riot police broke up an MDC press conference in a hotel believing it was an “unlawful” political gathering.

Mnangagwa, who hopes to attract private investors to Zimbabwe, has made strenuous efforts to improve the image of Zanu-PF, long seen as Mugabe’s political vehicle. Hundreds of international election observers were accredited for the first time for 16 years to monitor the campaign, which was largely peaceful in contrast to previous polls when there was systematic violence.

Authorities in Zimbabwe need international legitimacy to obtain the multibillion-dollar bailouts required to avoid economic breakdown. The high-profile violence is a serious setback and some say the crackdown suggests splits within the ruling elite.

Professor Stephen Chan, an expert in southern African politics at the University of London, said there were clear divisions among civilian officials, as well as tensions with parts of the military. “Some are leaning towards the harder line that Zanu-PF would have taken in the past. Others are more committed to the reformist re-engagement agenda.”

It is still unclear who ordered soldiers on to the streets on Wednesday. The troops that opened fire were from the presidential guard, nominally commanded by Mnangagwa but answering directly to Constantino Chiwenga, the former head of the military who led November’s takeover and was appointed vice-president in its wake.

“When you articulate a vision you don’t expect ... everyone to come on board … but I believe that the majority of my party members as well as the people of Zimbabwe will share [it] because it is based on modernisation, development, peace and security and unity,” Mnangagwa said last week.

The president insists the elections were free and fair, and says that monitors of the poll will help his government to learn from its mistakes. But observers have expressed concerns about a biased electoral commission, abuse of state resources, intimidation of voters and the voters’ roll.

“There will be some who are disappointed by the [election] outcome, but I urge everyone to remember that we are all brothers and sisters, sharing one dream and one destiny,” Mnangagwa said on Friday.

Members of the Movement for Democratic Change detained by police in Harare on Thursday. Photograph: Philimon Bulawayo/Reuters

MDC activists in the town of Chitungwiza, around 30km south-east of Harare, said yesterday that police and soldiers had moved through the St Mary’s and Ziko neighbourhoods in the evening on Friday . Both are opposition strongholds.

“They came in two waves. The first was just pushing people around, beating people with bars and sjamboks [leather whips]. Then later they had some kind of list and were going house to house looking for people. Luckily most people were already hiding,” one activist said. “We will continue the fight, of course. Mugabe stole decades of my life. We cannot give up now.”

In Chitungwiza, the army surrounded the house of a veteran MDC member of parliament. In Harare, troops and police sealed off the home of close relatives of former finance minister Tendai Biti.

In Harare, security forces conducted similar operations in Glenview and Glen Norah neighbourhoods.

“If this is what they are doing now, with all the observers and media here, imagine what they are going to do when no one is watching Zimbabwe any more,” another local MDC activist said.

Seven of those arrested on Thursday at the MDC headquarters were produced in Harare magistrates court yesterday but remanded in custody until this week.

Denford Halimani, their lawyer, called the decision “very unfortunate”.

A witness to Thursday’s raid told the Observer that the group were simply polling agents who had travelled to the MDC headquarters from polling stations to deliver hard copies of the count to enable the party to compile its own vote tally.

Letwin Mungoni, a friend of one of the accused, said they were being targeted simply because they were from the MDC. Amnesty estimate that there have been 60 arbitrary arrests in the last week.

The centre of the Zimbabwean capital was busy yesterday, with traffic and business near returned to normal. The army, a visible presence this past week, was no longer on the streets, though a military helicopter flew overhead. Two vehicles equipped with water cannon and an armoured vehicle full of riot police were stationed outside the MDC headquarters.

Most MDC supporters seemed resigned to the result and unwilling to take to the streets to protest. “We are just accepting whatever is there for the sake of peace, for the sake of business and calm,” said Shepherd Warikandwe, 38, a chef. “Life goes on. I wouldn’t support a protest. Check what happened this week when people tried it.”