President Robert Mugabe's government said aid groups would only be allowed to resume operations if they pledged not to interfere in politics, accusing them of openly siding with the opposition in the build-up to the ballot.
Authorities in Zimbabwe meanwhile accused the diplomats, whose dramatic detention triggered a furious response from Washington and London, of behaving like "common criminals" by refusing to cooperate with police at a roadblock.
In a country beset by food shortages, aid agencies have come to play a major role in both supplying and distributing staples such as maize and cooking oil.
Relations between Western charities and the Mugabe regime have long been strained, with the government previously forcing aid groups to channel their efforts through local officials.
However, the order to cease all field work marks a dramatic downturn in the relationship and comes only days after one of the largest aid groups, CARE International, was ordered to suspend its operations.
"As we speak there are no NGOs. All NGOs have been asked to reapply for registration," Deputy Information Minister Bright Matonga told AFP.
"They were involved in political activities and behaving like political parties when they were supposed to complement government efforts.
"As it appears that they veered from their normal work, we want them to clearly state what they intend to do, so that they will be bound by that."
While aid groups were reluctant to react to the order, the opposition Movement for Democratic Change (MDC) party said it was ridiculous to blame them for the government's unpopularity.
The MDC wrested control of parliament from ZANU-PF in a joint legislative and presidential election on March 29 in which Mugabe suffered the biggest blow to his authority since taking power at independence in 1980.
MDC leader Morgan Tsvangirai fell just two percentage points of winning an outright majority in the presidential poll on March 29 and now faces Mugabe in a second round run-off in three weeks' time.
"This is a sign of desperation," the party's chief spokesman Nelson Chamisa told AFP.
"It was the people of Zimbabwe who voted for the MDC. NGOs do not vote. It's condescending to think that the people of Zimbabwe voted on the basis of influence by NGOs."
As well as accusing aid groups of anti-government bias, the Mugabe regime has frequently accused Western powers such as the US and former colonial power Britain of siding with the opposition.
Mugabe himself accused the West of trying to "effect illegal regime change" during a speech at a UN food summit earlier this week.
According to Matonga, the detention of the diplomats at a roadblock on Thursday came after they had attended a gathering at the home of an MDC activist in the Bindura area, to the north of Harare.
Although it appeared two vehicles in the convoy managed to flee the roadblock, US ambassador James McGee said that one of the cars in the convoy had its tires slashed and threats were issued to set it alight.
Zimbabwe's national police spokesman Wayne Bvudzijena said the diplomats had only themselves to blame for not identifying themselves properly.
"We are surprised that the diplomats fled from Chipadze when they were asked to identify themselves by the police. In essence, they were reducing themselves to common criminals because if they had identified themselves there would have been no problems," he told the state-run Herald daily.
In Washington, US Secretary of State Condoleezza Rice told reporters that "the situation in Zimbabwe is really quite difficult and quite grave" ahead of the run-off election.
McGee said recent events showed there was little chance of the run-off being free and fair in rural areas but he said it was still essential that Tsvangirai ran in order to avoid handing victory on a plate to Mugabe.
In a newsletter on Friday, Tsvangirai - who was himself detained by police earlier in the week -- said most Zimbabweans wanted to see the back of Mugabe.
"In the depths of this trauma, we nevertheless welcome the opportunity on June 27 to again make a choice for change," he wrote.
"We know that all Zimbabweans want change except the very, very few vultures who are preying on the pain and suffering of the people."