He said he had to decide whether the rental contract was a bribe and a crime had been committed.
There are long waiting lists for flats in Stockholm and reports suggested the minister had special treatment.
One of Sweden's most outspoken figures, Ms Wallstrom has been at the centre of spats with Israel and Morocco.
She said she had nothing to hide about the rental agreement and said "it is good that this will be resolved".
Municipal workers' union Kommunal owns a number of properties in Stockholm and Swedish media have reported that Ms Wallstrom was offered a rental contract tied to her period in office.
Last week she said the union had assured her it had followed the rules and she was not jumping any queue when she took on the flat. "They lied to me about this," she told TT news agency.
Chief prosecutor Alf Johannson made clear there were no suspects at this point.
Stockholm has a widely known rental crisis. Waiting lists can last up to 13 years in the centre of the city and nine years in other districts.
Ms Wallstrom has become a high-profile but controversial political figure in Sweden.
Last year, she was accused by Saudi Arabia of "blatant interference" in its internal affairs after she criticised its human rights record.
She cancelled a trip to Israel last week after infuriating Prime Minister Benjamin Netanyahu when she called for an inquiry into whether Palestinian knife attackers had fallen victim to extrajudicial executions.
Some 145 attackers have been fatally shot in four months of violence and at least 100 of them had carried out attacks, Israel says. More than 25 Israelis have died.
She also cancelled a visit a year ago, weeks after Sweden's centre-left, Social Democrat-led government officially recognised Palestine.
Last week the Stockholm government decided against officially recognising Western Sahara as an independent republic in an attempt to end a row with the Moroccan government.
Reports in Sweden linked the change of heart to a decision by the Rabat government in September to block the opening of Morocco's first Ikea store.
Sweden's anti-corruption prosecutor has launched an investigation into a union flat in Stockholm rented by Foreign Minister Margot Wallstrom.