The army has not yet found the missing boys
The Ugandan army is still seeking a group of rebels who abducted more than 40 trainee Catholic priests over the weekend.
Army spokesman Major Bantariza told BBC News Online that at least 100 soldiers had been sent to rescue the boys.
An eight-year-old boy was shot dead during the attack, which happened early on Sunday morning at the Lacor junior seminary in Gulu district, about 400km north of Uganda.
The LRA rebellion has lasted 16 years, during which time thousands of children have been abducted and conscripted to fight alongside the rebels.
The director of Lacor seminary, Mathew Odong, told the BBC's Network Africa programme that he fears those abducted may be forced to become LRA fighters.
The archbishop of the diocese, John-Baptist Odama, told the French news agency, AFP, that the rebels smashed their way into the dormitory and abducted 44 boys aged between 12 and 18.
He said that three of the students later escaped their captors and returned to the seminary.
Major Bantariza said that he had no information on reports that a group of 700 LRA fighters may have fled their bases in southern Sudan following a suspected outbreak of the deadly Ebola disease there.
He said they were always moving between southern Sudan and northern Uganda.
The government last month ended its six-week truce after accusing the LRA of continuing its attacks and abductions.
The truce was intended to smooth the way for peace talks between the government and the rebels.