PCB chairman Shaharyar Khan also denied having differences with Raja or that it had been decided to replace him with a former bureaucrat Abu Shamim Arif.
"The PCB emphatically denies reports that refer to imminent changes in the PCB hierarchy. The Board also denies speculation of differences between the chairman and chief executive," a press statement from the PCB said.
Local daily The News quoted a spokesman of the Board as saying the reports were baseless and unfounded.
"The chairman wanted to have the situation cleared after several reports on this issue," he said.
A section of the local media had reported on Friday that Raja was on his way out as the PCB chief was unhappy over his dual role as a TV commentator and CEO.
Meanwhile, PCB treasurer Naeeem Ahmad has quit after levelling charges of irregularities against the Board officials. Ahmed has reportedly submitted his resignation letter to the PCB chief.