Police spent hours checking documents at the 1MDB fund's Kuala Lumpur office.
Mr Najib denies allegations that nearly $700m were transferred to his personal bank accounts from the fund.
On Tuesday officials froze six accounts as part of the inquiry. The account holders were not identified.
But the country's attorney general has since clarified that none of the accounts frozen were ones allegedly held by Mr Najib.
The 1MDB fund said it was co-operating with the police investigation.
"We can confirm that a number of officials from the task force, conducting an inquiry into 1MDB, visited our offices today," it said in a statement.
"They were provided with a number of documents and materials to aid with the investigations currently taking place."
The fund, set up by Mr Najib in 2009 and still chaired by him, denies giving any money to the prime minister.
Meanwhile, in a BBC interview, Malaysia's former leader Mahathir Mohamed called on Mr Najib to show public proof that his assets are legal.
Correspondents say he is facing the biggest crisis of his political career - pressure has been mounting since the Wall Street Journal published a detailed report last week. He was already under fire over his leadership, particularly from Mr Mahathir.
Mr Najib has previously issued a statement on Facebook, saying that the various allegations made against him are "unsubstantiated" and "outrageous".
He accuses Mr Mahathir of trying to topple him and describes his former mentor's claim that 42bn ringgits ($11bn) have gone missing from the fund as "reckless".
"These are audited debts backed by 51bn ringgits [in] audited assets." Mr Najib said in his Facebook post.
The authorities in Malaysia have raided the office of a state investment fund as part of investigations into claims of corruption involving Prime Minister Najib Razak.