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Mr O'Farrell said he had spoken to Prime Minister Julia Gillard about the potential crossover between the two inquiries.
He also gave Ms Gillard assurances that state agencies would fully co-operate with the federal government as it develops its terms of reference.
The issue of child abuse was reignited after Detective Chief Inspector Peter Fox penned an open letter last week to the premier alleging cover-ups by the clergy and police, after spending decades investigating clergy abuse around Newcastle.
Mr O'Farrell subsequently announced a state inquiry, but on Tuesday he said it probably wouldn't go ahead if Mr Fox's allegations were incorporated in the national royal commission.
"What we don't want to do is have inquiries falling over each other," he told reporters.
"I want to engage with the prime minister for the terms of reference for her royal commission.
"If those terms of reference cover the issues raised by Peter Fox, we will reconsider our commission."
Mr O'Farrell added he did not want investigations into the allegations of abuse delayed.
"A matter of weeks is acceptable, but I wouldn't like to see it pushed back to next year," he said.
