The agency now says it is calculating on 60,000 refugees making their way to Sweden, or 100,000 at the very most.
Previously it had set 140,000 new arrivals as the upper limit.
“We see every day how people are making their way from Turkey to Greece or across the sea to Italy, but they are not currently reaching Sweden,” said the agency’s operations manager, Mikael Ribbenvik, in a statement.
The agency also revised downward its estimate of how much money it would need after the historic spike in asylum seeker arrivals last autumn. With fewer applications expected this year, the agency wants 54.7 billion kronor ($6.7 billion) from the government to fund its operations, a drop of 6.4 billion on the previous forecast.
A country of 9.8 million, Sweden took in more than 160,000 asylum seekers in 2015, putting it among the EU states with the highest proportion of refugees per capita.
In October 10,000 refugees were arriving every week. The figures dropped sharply at the start of this year as Sweden and other EU countries tightened border controls, while poor weather conditions in the Mediterranean led to fewer crossings.
Since the migration agency made its last prediction in February the so-called Balkan Route has become impenetrable for refugees and a controversial EU deal has come into force that keep more asylum seekers in Turkey.
In the first three months of this year 9,000 people applied for asylum in Sweden, compared to 13,000 in the same period last year.
The United Nations refugee agency UNHCR says the number of refugees arriving in Greece from Turkey has fallen from 870 a day in March to 130 a day in April.
The reduction is mainly attributed to the EU-Turkey deal, which returns refugees from Greece to Turkey unless they want to apply for asylum in the EU country. Most don’t, as this would prevent them from submitting applications in countries like Germany and Sweden which are seen as being more attractive.