The South Korean champions said the payments were made on a personal basis and the sums involved were too small to be considered bribes.
Prosecutors said two referees have been charged with accepting bribes totalling 5 million won ($5,800), with a club scout making three payments to one official and two to the other, each for 1 million won ($1,160), in 2013.
The case had been sent to the courts for trial next month, Busan District Prosecutor's Office said.
Korea's Yonhap News quoted prosecutors as saying the referees had already been sentenced to jail time for involvement in a bribery scandal last year, when it emerged the former president of Gyeongnam FC had paid tens of thousands of dollars to referees to award favourable decisions.
However, Jeonbuk Motors official Kim Sang-soo said this case was different.
"Yes, money was handed over but the scout and referees knew each other from outside the game," Kim was quoted saying by RAW, insisting referees do not make much money and the scout was helping them out in tough times.
"The amounts were for around 1 million won (each time). It's not really on a scale where you can say it was a bribe and there was something expected in return."
Kim said the club should have been more careful at a management level but that the scout did not feel he had to report what had been a private matter.
"The two referees were on the field for eight of our games," Kim said.
"We had three wins, two losses and three draws, so it doesn't really make sense to say the scout bribed the referees."
A Korea Football Association spokesman said they were conducting their own investigation.