"The pilot successfully ejected and the plane crashed thereafter within Tengah Air Base," it said in a statement.
"The pilot is conscious and able to walk. He is receiving medical attention and no other personnel are hurt."
The ministry said the Singapore jet "experienced an issue during take-off and the pilot responded in accordance with emergency procedures."
It added that it had begun investigating the crash.
Such incidents are extremely rare in the city-state with the most advanced air force in Southeast Asia.
"The last time we had a fighter jet crash incident was 20 years ago," Defence Minister Ng Eng Hen said on Facebook, referring to a 2004 incident that happened in Arizona in the United States during training.
"It's a credible record but (I'm) obviously disappointed over this incident," he said adding the goal for the Republic of Singapore Air Force "must still be zero crashes".
In 2010, a military helicopter made an emergency landing at an open field near a Singapore residential area due to issues with the engine.
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