The newspaper said its three-month investigation suggested that Iran's ostensibly peaceful commercial nuclear program "masks a plan to become the world's next nuclear power."
The newspaper said the use of scientists and technology from Russia, China, North Korea and Pakistan had brought Iran much closer to building a nuclear bomb than Iraq had ever been.
The Times reported that Iran has several weapons research laboratories at a plant disguised as a watch-making factory.
The newspaper also said Iran had secretly imported 1.8 tons of nuclear material from China in 1991, and used some it it to make uranium metal, which would only be useful for weapons production.
The U.S. and other Western nations have expressed deep concerns about Iran's nuclear program.
Iran has repeatedly denied that it is building a nuclear weapon and did so again on Monday.
On a visit to the Philippines, Iran's Foreign Ministry spokesman, Hamid Reza Asefi, again rejected U.S. claims that his country is involved in clandestine nuclear weapons programs, saying, "We are not looking for any military nuclear activity."
"That is out of the question. ... We are not thinking that way," he said. "We are having a very good cooperation with the International Atomic Energy Agency. We are ready to continue that."
Iran, which insists its nuclear program is for peaceful, electrical power purposes, has said it would agree to unfettered inspections by the Vienna-based IAEA if it is granted access to advanced nuclear technology as provided for under the Nuclear Nonproliferation Treaty. Tehran says Washington's influence is blocking that technology.