Mr Bildt said he had been given no explanation
Sri Lanka has refused entry to Sweden's Foreign Minister Carl Bildt.
Mr Bildt was to have taken part in a European diplomatic mission. He is recalling Sweden's top diplomat in Sri Lanka for consultation.
The UK's David Miliband and France's Bernard Kouchner will still go on the mission, which is expected to push for a truce between the army and rebels.
Sri Lanka's foreign ministry said this was not a snub and it could only cope with so many high-level delegations.
Sri Lanka has had tense relations with the Scandinavian former monitors of its peace process but its main problems have been with the major ex-mediator, Norway.
Mr Miliband and Mr Kouchner are both expected to arrive on Wednesday.
Mr Bildt told the BBC: "They have said I am not welcome at this particular period of time - they were saying that they can't handle too many people.
"There must be some sort of reason but it has to be a rather odd one."
Mr Bildt said he was recalling the Swedish ambassador in Sri Lanka for consultation, adding that Sri Lanka did "not seem to be too interested" in its relationship with Sweden at the moment.
However, he insisted it was right for the mission to continue.
"Even if only one of us were able to go it would be worth it because we really need to try to pressure everyone to allow international access [to civilians]."
The UN's John Holmes has visited civilian camps in Vavuniya
Karel Schwarzenberg, the foreign minister of the Czech Republic, which holds the rotating EU presidency, said the Sri Lankan move was "a grave mistake... which will of course have repercussions in Europe".
Sri Lanka has tried to play down the incident.
Foreign Secretary Palitha Kohona told Reuters: "We have not rejected the Swedish foreign minister. He has been invited to come here next week because we are just overwhelmed at the moment with all these visitors."
He said of possible repercussions: "Mature governments and institutions should not deal with each other based on threats."
The BBC's Charles Haviland says officials in Colombo are calling this a "non-issue" but he says the diplomatic spat is a symptom of tension between EU countries and Sri Lanka.
EU foreign ministers on Monday joined the UN in calling for a ceasefire in the north-east, where the army is battling the rebels.
Diplomatic efforts to bring more help for the civilians in the war zone have so far made little progress.
The United Nations top humanitarian envoy, John Holmes, said on Monday that he had failed to secure agreement from the government on access to civilians.
The Sri Lankan military has restricted the rebels to a 12 sq km (5 sq m) area of land and believes final victory is near.
On Monday the Sri Lankan government said it would stop using heavy weapons in the war zone and that its operations were drawing to a close.
However, a Tigers spokesman in the conflict zone, Puleedevan, told the BBC that troops had begun mortar, artillery and rocket fire early on Tuesday morning.
Speaking for the Sri Lankan army, Brig Udaya Nanayakkara said no heavy weapons had been used.
There is no way of confirming the reports as independent journalists are denied access to the war zone.
The Tamil Tigers have fought for an independent homeland for Sri Lanka's Tamil minority since 1983.
More than 70,000 people have been killed in the war, but that figure could now be far higher.