Citing unnamed government officials, the newspaper said one senior official described the secret memorandum, which was written in January, as "a wake-up call."
According to the report, the document sparked efforts in the Pentagon, the White House and the intelligence agencies to develop new options for President Barack Obama.
They included secret military operations against Iran if international sanctions failed to force the country to change its approach, the paper said.
Gates wrote in the memorandum about several of his concerns, including a scenario that many experts consider the most likely, The Times said.
Under this scenario, Iran would assemble all the major parts required but stop short of actually making a fully operational weapon.
In that case, Iran could remain a signatory of the Nuclear Nonproliferation Treaty while becoming what experts call a "virtual" nuclear weapons state, the report said.
The memorandum also urged the White House to think about how the United States might contain Iran if it decided to produce a weapon; and how to deal with the possibility that nuclear fuel or weapons could be obtained by one of the militant groups Iran supports, the paper said.
