Scott Morrison's account on the Chinese social media platform was taken over and rebranded to "Australian Chinese new life" earlier this month, according to the Daily Telegraph.
Mr Frydenberg says it's not good enough the Labor leader still had access to WeChat while the prime minister did not.
"It's something we would like to see rectified because it's a method of communication to the Australian Chinese community which is very important," he told reporters in Brisbane on Monday.
"It should be on offer to politicians of all political persuasions, it shouldn't be a political football. It's very, very disappointing to see the prime minister prevented from having that access."
But Mr Frydenberg didn't join his colleague's call to boycott the platform amid the controversy.
Liberal chair of the parliamentary intelligence and security committee James Paterson said WeChat had not heeded requests from the government to restore access to Mr Morrison's account.
He called on all Australian politicians to boycott the platform.
"The government has directly appealed to WeChat to restore access and no response has been given, which seems pretty clear WeChat has no intention on allowing the prime minister to continue to post," he told Sky News.
Senator Paterson said the action was sanctioned by the Chinese government and amounted to foreign interference.
"What the Chinese government has done by shutting down an Australian account is foreign interference of Australian democracy in an election year," Senator Paterson told Sydney radio station 2GB.
"It is very clearly government action in my view. No politician should be on WeChat and legitimising their censorship."
The Victorian senator also revealed the prime minister's WeChat account has been plagued with problems for at least six months, with issues starting around the time he attended G7 meetings in the UK.
An agent running Mr Morrison's account due to the app's terms and conditions experienced trouble posting in the middle of 2021, which was around when the prime minister lobbied global government heads not to become overexposed to Chinese influence.
The initial problems came as he took a list of 14 demands handed by the Chinese embassy to an Australian journalist to the G7 to warn world leaders about the dangers of giving China too much leverage.
"It wouldn't be at all surprising if those two events were connected," Senator Paterson said.
He said it was also concerning 1.2 million Chinese Australians who use the service couldn't access news from the prime minister, but could still see government critiques on the platform from Opposition Leader Anthony Albanese.
He said Mr Albanese shouldn't allow a foreign government to dictate the terms of Australian debate or dictate how a prime minister can speak to his own people.
"A relatively small number (of politicians) are active on the platform and I think that is appropriate given that it is a surveillance and monitoring platform of overseas Chinese," Senator Paterson said.
"Now that they are attempting to make a partisan intervention by blocking one side of politics getting out a message on there, it is incumbent on all politicians to get off the platform."
Liberal MP and former diplomat Dave Sharma also said the move was likely sanctioned by the Chinese government.
Mr Sharma says while the prime minister was right to have a WeChat account to connect with Australia's Chinese diaspora, the platform was ultimately controlled by the Chinese communist party.
"More likely than not it was state sanctioned and it shows the attitude towards free speech and freedom of expression that comes out of Beijing," he told Sky News.
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