Secret film of the policy in action added to racism claims
The measures are being described as an attempt to prevent any potential abuse of Britain's asylum system - but critics say they target Roma, or gypsies, in a policy which amounts to racial discrimination.
Controversy had deepened when a Roma journalist was secretly filmed being turned away, while his non-Roma colleague - with identical travel plans - was allowed on her way.
But the British Embassy said an increase in asylum claims since the suspension had made it necessary to resume the checks at Prague's Ruzyne Airport.
The Czech authorities have agreed to the system because the alternative could be the imposition of visas for all Czechs travelling to the UK.
If that happened, it would be seen as a serious setback for Czech efforts to join the European Union, and the Czechs fear that other EU member states might follow suit.
With the checks resumed, British immigration officers are now examining the papers of all passengers travelling to any UK airport.
The BBC's Ray Furlong in Prague says the officers are, in effect, deciding who can get on a plane to London and who cannot.
Those allowed to travel are given boarding cards, allowing passengers to check in as normal for their flights. Those without cards are turned away from the check-in desks.
Many asylum applications are made by Roma - commonly known as gypsy - families.
"The first round of controls was very effective in reducing such claims for the three weeks they were in operation, and for some time afterwards," the British Embassy said in a statement.
"But recent arrivals have made it clear that it is necessary to repeat the operation in order to demonstrate that the UK is not prepared to tolerate further abuse of its asylum system."
It said the controls would be "non-discriminatory" and would apply to all passengers of whatever nationality.
Few granted asylum
Bona fide travellers to the UK were welcome and "would find the pre-clearance makes procedures on arrival in the UK much easier", the embassy added.
All passengers on flights to London - including British nationals and passengers from other European Union countries and the United States - will be subject to the checks.
Those who give unsatisfactory answers to immigration officers may be turned away.
Last year, 1,230 people arriving from the Czech Republic claimed asylum in Britain, and 515 applications had been received by the end of May this year.
The number of successful applications is "very small," a Home Office spokeswoman said.
Last week, more stringent immigration checks at Prague airport led to a number of Roma families, including one made up of more than 10 members, being turned away.
Discrimination complaints
There are estimated to be approximately 200,000 Roma gypsies in the Czech Republic - nearly 2% of the population.
Roma people often complain of discrimination and suffer frequent racially motivated attacks and high unemployment in the Czech Republic, and elsewhere in eastern Europe.
They often leave for the West, mostly Britain, in hopes of a better life.
But a Home Office spokesman said there is virtually no chance for a Czech citizen being granted asylum in the UK because the authorities do not believe they are subject to persecution by the state.
Instead, both the Czech and the UK governments see them as economic migrants.