The fund's announcement came in the wake of last week's move by the U.S. Department of Justice to seize more than $1 billion worth of assets it alleged were tied to an international conspiracy to launder money funneled away from 1MDB.
As well as giving notice of Deloitte's intention to resign as auditor of the fund, 1MDB said in a statement posted on its website on Tuesday that it "remains confident" that the fund committed no wrongdoing and that previous audited statements were "true and fair."
But it added that as "a precautionary measure," the 2013 and 2014 audited statements shouldn't be relied on until the allegations in the U.S. complaint were resolved.
Deloitte echoed that view, saying in a statement dated Tuesday that if the information in the U.S. complaint had been known during the 2013 and 2014 audits, it would have impacted the financial statements and audit reports Deloitte signed off on for those years.
The accountancy firm added that 1MDB hadn't yet informed Deloitte Malaysia that it had appointed any new auditor.
Three of the Big Four accounting firms appeared to have walked away from their work at 1MDB.
In February 2014, the Malaysian fund issued a statement saying that it "mutually agreed with KPMG that the firm would cease to be 1MDB's auditors" and that Deloitte would take over the role.
The statement at the time said KPMG had signed off on the 2010, 2011 and 2012 accounts, but that Deloitte would complete the audit for the financial year ended March 31, 2013. 1MDB said that it had received an extension until the end of March of 2014 to file those annual statements.
The 1MDB statement from February 2014 added, "this is nothing special or new as it is in line with best market practice where companies decide on its current or future auditors after considering all aspects, including but not limited to conflict of interests and other consideration."
According to a Wall Street Journal report on Tuesday, however, the Malaysian auditor general found in 2015 that Malaysian Prime Minister Najib Razak, who chaired 1MDB's board of advisers, had fired KPMG at the end of 2013 for balking at approving the fund's accounts.
KPMG didn't immediately return an emailed request from CNBC for comment.
Multiple media reports had said that EY, another Big Four firm, which was the auditor for 1MDB and its predecessor fund from 2009-2010, had also been sacked by the wealth fund in 2010 after also raising concerns over the accounts. EY didn't immediately return an emailed request for comment.
The fourth of the Big Four accounting firms, PwC, didn't immediately return an emailed request for comment on whether had worked for 1MDB or would consider stepping into the role of auditor.
Questions about the movement of funds from 1MDB first gained widespread attention around a year ago, when the WSJ reported that in 2013 nearly $700 million had flowed from the fund to Prime Minister Najib's personal bank account.
Najib has repeatedly denied wrongdoing and in January Malaysia's Attorney General Mohamed Apandi Ali said that the funds in question were a gift from Saudi Arabia's royal family, the majority of which had been subsequently returned.
Apandi said that no criminal offense had been committed.
But globally, investigations into 1MDB's financial transacitons in locales as varied as U.S., Switzerland, Singapore and the Seychelles have continued.
Announcing the asset seizure case last week, the U.S. Department of Justice said officials at 1MDB, their relatives and other associates diverted more than $3.5 billion from the state fund and laundered it through complex transactions with international shell companies.
The DOJ complaint did not identify Najib by name, but both the WSJ and Reuters reported that "Malaysian Official 1," who according to the DOJ's filing allegedly recieved hundreds of millions of dollars from 1MDB, was the Malaysian Prime Minister.
At the time, the Najib's office said in a statement, "As the Prime Minister has always maintained, if any wrongdoing is proven, the law will be enforced without exception."
Meanwhile, Singapore's central bank last week said that it found "lapses and weaknesses" in anti-money-laundering controls at the Singapore operations of several banks in their dealings with 1MDB.
—By CNBC.Com's Leslie Shaffer; Follow her on Twitter @LeslieShaffer1