There were a total of 513 hate crimes motivated by sexual orientation or sexual identity reported to police in 2014, a 13.5 percent increase over the previous year, the ministry said in a report.
The vast majority of the victims, 72 percent, were women.
Hate crimes motivated by race accounted for 37 percent of last year's tally, while those that targeted disabled people accounted for 15.5 percent.
The total number of hate crimes reported last year was 9.6 percent higher than the figure for 2013, the first year Spain collected figures.
The interior ministry said the rise was due to more complete record-keeping and the fact that more people feel comfortable coming forward, the ministry said.
Interior Minister Jorge Fernandez Diaz said last year's figures did not include complaints made to the regional police force in the northern Basque Country for "technical reasons".
The publication of national hate crime figures last year for the first time helped throw the spotlight on the problem, leading more people to feel comfortable to file complaints, he added.
A quarter of the victims of the hate crimes reported last year were under the age of 18.
In most cases the culprits were identified.
"Impunity for hate crimes does not exist," the interior minister said.