The government appointed a panel to look at Panama`s financial practices.
But Mr Stiglitz and Swiss anti-corruption expert Mark Pieth, who also quit, said government interference in their work amounted to "censorship".
The seven-person panel also included Panamanian experts.
"I thought the government was more committed, but obviously they`re not," Mr Stiglitz told Reuters news agency. "It`s amazing how they tried to undermine us."
A statement by Panama`s Ministry of Foreign Affairs said "the Panamanian government understands both resignations and internal differences", adding that it maintains a "real commitment to transparency and international co-operation".
The ministry said it had already acted on some recommendations made in the panel`s preliminary report and was considering others, without specifying which measures had been taken.
But a statement by Mr Stiglitz and Mr Spieth to Reuters said they were concerned that the panel`s final report would not be published.
"We can only infer that the government is facing pressure from those who are making profits from the current non-transparent financial system in Panama," Mr Stiglitz said.
The Panama Papers were investigated for months by hundreds of investigative journalists, including staff from the BBC.
The documents, which were first detailed in April, revealed the hidden assets of hundreds of politicians, officials, current and former national leaders, celebrities and sports stars.
They list more than 200,000 shell companies, foundations and trusts set up in tax havens around the world.
Mossack Fonseca said it had been hacked by servers based abroad and filed a complaint with the Panamanian attorney general`s office.
The company said it did not act illegally and that information was being misrepresented.
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