The Equality Commission said just 44% of people are aware of how the law could protect them against intolerance on the grounds of sexual orientation.
It was reported that a significant level of prejudice still exists against members of the gay, lesbian and bisexual community in NI.
However chief commissioner Michael Wardlow said transphobic incidents have been some of the most severe.
"The highest level of negativity was reserved for the smaller minority of people who struggle with their gender identity - trans people," he said.
"Everyone has the same rights under our equality and hate crime laws to lead a life free from discrimination, abuse or harassment. But prejudice is still rife."
According to the PSNI there were 246 homophobic incidents in the past year.
The figure is up by 46 (23%) on 2012.
Incidents described as transphobic jumped from four to 15 over the last year and there were a further six transphobic crimes - a 100% rise from the three the previous year.
The figures were released as part of Anti-Homophobia week.
Mr Wardlow added that the commission receives 3,000 queries a year but just 2.5% concerned sexual orientation and even fewer related to gender identity.
He said: "We have already recognised the need to take special measures to address under-reporting of sexual orientation discrimination here in Northern Ireland.
"We know that we need to make particular efforts to reach out to LGBT individuals who may feel that they are totally alone and that they have no recourse against unfair treatment. These are the people who could really benefit from our staff's advice, support and experience. And individuals can be reassured of receiving a confidential and supportive response when they seek our help."