The National Anti-Corruption Unit (Riksenheten mot korruption) is now looking into the case, and will be investigating if Juholt's actions constitute fraud.
"I didn't know the rules," he said on Friday.
But Juholt was already informed about them this summer, according to the Riksdag Administration.
"I didn't know what the rules were, and I'm sorry about that," said Håkan Juholt to the large press gathering at the Social Democrats' headquarters on Friday.
Swedish MPs are reimbursed for their overnight accommodation in Stockholm if they hail from another part of the country. If the apartment is shared with another person, the Riksdag foots half the rent.
Juholt is registered in Oskarshamn, in southern Sweden, but has been pocketing full reimbursement for a four-room apartment in southern Stockholm - even though he shares it with his girlfriend.
"It never occurred to me that I could've been doing something wrong," said Juholt.
According to the paper Riksdag & Departement, the Riksdag Administration have calculated that Juholt has been given 320,532 kronor for his living costs, since February 2007. This would mean that Juholt owes roughly 160,000 kronor, for the half of the rent that his partner ought to have paid.
On Saturday, most opinion pieces in Swedish media seemed to buy Juholt's excuse that he was unaware of the rules, but many question his competence and reliability as a party leader.
"It may be human to err, but the whole business is very embarassing," wrote newspaper Borås Tidning, whose opinion page is Moderate-leaning, adding: "Everyone can make a mistake, but politicians on Juholt's level need to act differently and be more aware."
Juholt maintains that he hasn't withheld any information, or tried to hide anything.
"What keeps falling back to me is that I didn't know that rule."
But Riksdag Administration's department head Marianne Bjernbäck stated that she contacted one of Juholt's assistants as early as the end of July or the beginning of August, to ask if the Social Democrat head was to continue claiming reimbursements for the entire rent.
The Riksdag Administration had reacted upon hearing through the media that Juholt lived with his girlfriend, and wanted to ensure that the party leader was receiving the correct reimbursement.
Despite this, Juholt went on to claim reimbursement in the same way as before on 13 September.
"Of course we don't reimburse anyone other than MPs," said Bjernbäck to news agency TT.
When previous Social Democrat leader Mona Sahlin was discovered to have been careless with credit cards and her own economy in the 1990s, she took a time-out and missed the opportunity to become party leader for some time.
But female politicians are judged harsher than male, believes political scientist Jenny Madestam.
"Women and men are measured with different yardsticks, of course. I haven't kept track of all the drama surrounding Juholt, but if he has consciously tried to commit fraud, it's obviously a problem. Swedes dislike when those in power line their pockets. Confidence for Håkan Juholt may be shaken again," said Madestam to TT.