His warning comes less than a month after violent protests broke out over the arrival of 100 refugees in Casale San Nicola, a suburb in the outskirts of the city.
Concerned about how to accommodate more refugees, Marino said the city is "overcrowded".
"We can't welcome 18 to 20 percent of people who arrive in our country. We don't have the resources,” he was cited by Ansa as telling a Lower House commission on immigration on Tuesday.
With reception centres bursting at the seams, refugees set up a makeshift camp outside Rome's Tiburtina station in mid-June before it was raided by police.
Several leaders in Italy's wealthier north have refused to bow to a government call to take in more refugees, but this is the first time concerns have been voiced by the Rome mayor.
But tensions over immigration have escalated across Italy in recent months. A day before the Rome protests, residents in a Treviso district burnt furniture intended for refugees in protest against their arrival. The refugees were eventually taken to an empty police station outside the city.
Marino is also under pressure to fix the city's myriad other problems, including its transport system, the maintenance of monuments and its waste issue.