Salles, one of the most controversial figures in Bolsonaro's government, has presided over a surge of deforestation in the Amazon rainforest, and activists accuse him of dismantling Brazil's environmental protection programmes.
Brazilian media reported police had searched Salles's home in Sao Paulo as part of the operation.
Under the alleged scheme, IBAMA waived requirements for timber exporters, and granted retroactive authorisation to thousands of wood shipments exported in violation of environmental regulations in 2019 and 2020.
Some of the shipments had been seized by US and European authorities.
IBAMA allegedly instituted the policy over the objections of its own staff shortly after Salles and Bim met with representatives of three companies whose shipments had been seized.
Moraes's ruling revoked the IBAMA policy with immediate effect.
However, Salles, 45, denied wrongdoing. "These alleged acts never happened," he told journalists.
The news was the latest blow to Brazil's environmental track record under Bolsonaro.
The destruction of the Amazon, a vital resource for curbing climate change, has accelerated in Brazil since the former army captain took office in 2019.
Deforestation in the Brazilian Amazon surged by 85 per cent in his first year in office, destroying an area bigger than Puerto Rico, according to government data. It has continued at a high rate since, last month setting a new record for April at 581 square kilometers.
Activists and experts say Salles has facilitated environmental destruction rather than fighting it.
The Climate Observatory, a coalition of Brazilian environmental groups, said Salles had "acted against the environment from the day he set foot in his ministry."
"The fact is that Salles set up an all-out environmental crime office right in the environment ministry. And one day, he'll have to pay the price," said executive secretary Marcio Astrini.