The attack came shortly before Iran was due to take part in talks aimed at reviving the 2015 nuclear deal with the US, UK, France, China, Russia and Germany.
"We are nonetheless pleased that Iran has continued to agree to engage in discussions", Biden said at a joint news conference with Japanese Prime Minister Yoshihide Suga.
While 60 per cent is higher than any level Iran previously enriched uranium, it is still lower than weapons-grade level of 90 per cent.
A 2015 deal with world powers to rein in Iran's nuclear ambitions in return for the lifting of sanctions had capped the level of purity at 3.67%.
An annual United States intelligence report released this week maintained that "Iran is not now undertaking the key nuclear weapons-development activities that we judge would be necessary to produce a nuclear device".
The head of the Atomic Energy Organisation of Iran, the country's civilian nuclear arm, later acknowledged the move to 60 per cent, according to state TV. "But we have to work on arrangements to drop it to 5 grams per hour". "But then we will simultaneously produce 20% (uranium)", Salehi said.
Earlier, parliament speaker Mohammad Qalibaf said Iranian scientists had successfully started enriching 60 percent uranium at 12:40 am local time (0810 GMT).
"The will of the Iranian nation is a miracle-maker and it will defuse any conspiracy", Mr Qalibaf said on state television.
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Negotiators are trying to get both Iran and the U.S. to fully recommit to the deal, which would mean Iran coming back into compliance and the United States easing sanctions that have crippled Iran's economy.
Iran insists its nuclear program is peaceful, though the West and the IAEA say Tehran had an organized military nuclear program up until the end of 2003.
Biden said on Friday he thinks it is premature to make a judgment as to what the outcome of the talks will be, but the countries are still talking.
That cast a shadow over the talks in Vienna aimed at rescuing a nuclear agreement between Iran and world powers that the United States ditched nearly three years ago. "Obviously this is not making the negotiation easier", the European Union official told reporters, calling what happened at Natanz "deliberate sabotage".
Abbas Araqchi, Iran's chief nuclear negotiator in Vienna, said earlier this week that Iran would activate 1,000 advanced centrifuge machines at Natanz.
A senior Iranian official has admitted that Israel stole the archive of his country's nuclear programme in an alleged Mossad operation carried out in 2018, Israeli newspaper The Jerusalem Post reported on Thursday.
"The country has been widely exposed to security violations, and the example is that in less than a year, three security incidents have occurred: two explosions and one assassination", explained Rezaei. Iranian authorities have accused Israel of "sabotage".