In a statement the ministry said the attempt was made on Sunday night in Taichung prison in central Taiwan.
The statement added that he had used a towel in the attempt but was stopped by guards in a prison bathroom. He is now said to be in a stable condition.
Chen Shui-bian, 62, was the island's president from 2000-2008. He is serving a sentence for corruption offences.
According to the statement, Mr Chen said he tried to take his own life to protest against his conviction.
"No serious abnormalities were found after a health check," the justice ministry said.
The jail had arranged for a psychologist to see Mr Chen and his mood was "gradually improving", it added.
Mr Chen had been receiving medical treatment in recent months for health problems, which according to local reports include severe depression.
His office has been seeking medical parole for him.
The former president, who angered Beijing while in office by pushing for Taiwan's independence, was jailed in 2009 for corruption.
In 2011 he was given an additional sentence for money-laundering and forgery. He says the charges are politically motivated and a punishment for his pro-independence stance.
Chen's election as president ended more than 50 years of rule by the Kuomingtang, which is now back in power.
Taiwan's imprisoned former President Chen Shui-bian has tried to take his own life, the justice ministry says.