In a televised speech at an anti-corruption event in Tehran, he said money once “given under the table now is being given on the table”.
Mr Rouhani also called for the “elimination” of monopolies.
A series of high-profile corruption cases have come to light since his government took office in August 2013.
In May, the billionaire businessman Mahafarid Amir Khosravi was executed after being convicted of being behind a scandal involving embezzlement, bribery, forgery and money-laundering that cost 14 state-owned and private Iranian banks nearly $2.6bn (£1.7bn).
And in September, former Vice-President Mohammad Reza Rahimi was reportedly imprisoned after being convicted of corruption.
Mr Rahimi was reported to be linked to another billionaire businessman, Babak Zanjani, who has been accused of skimming up to $2.7bn (£1.7bn) of revenue generated from selling Iranian oil on behalf of the government through his companies to bypass international sanctions.
In his speech, President Rouhani called on Iranians to “apply all our power in fighting corruption.”
“The continuation, the deepening and the expansion of corruption is endangering… the Islamic Revolution.”
Mr Rouhani also criticized monopolies – on anything from the production of rifles to advertising – which he said were the cause of corruption.
“Anything which does not have rivalry or whose management is monopolized is flawed,” he said.
“This is wrong and the problem has to be uprooted,” he added.
Analysts said this might be a veiled reference to the Islamic Revolution Guards Corps (IRGC), which has become a major military, political and economic force in Iran since being set up after the 1979 revolution to defend the country’s Islamic system.
The IRGC is said to control around a third of Iran’s economy through a series of subsidiaries and trusts, and is widely believed to engage in illicit and black-market activities.
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