The development came as a bench headed by Justice R.F. Nariman and comprising Justice S. Ravindra Bhat observed that a charge sheet had already been filed and the matter assigned to a sessions court for trial.
The Karnataka government counsel told the apex court that the state High Court too had stopped monitoring the case's progress.
The apex court observed that the status report filed by a Special Investigation Team had said that two of the main accused in the case were absconding and cannot be traced.
Kalburgi, a former Vice Chancellor of Hampi University and well-known epigraphist, was gunned down at his residence in Kalyan Nagar in Dharwad on August 30, 2015. He was a Sahitya Akademi award-winning writer of old Kannada literature.
Last year, the top court had directed the Karnataka High Court's Dharwad bench to monitor the case probe.
The case was taken over by Karnataka police SIT, which also investigated the Gauri Lankesh murder case, and filed the charge sheet.
Umadevi Kalburgi, the wife of the slain rationalist, had moved the apex court for a fair probe, alleging a link between the murders of her husband, rationalist Narendra Dabholkar and social activist Govind Pansare.
She had pleaded for the probe's transfer to a central agency.
The top court had said that if these killings are linked, one agency should probe them and that it should be monitored by the High Court.
The Maharashtra Police SIT was probing the killing of Pansare in 2015 whereas the CBI was investigating Dabholkar's murder.
Kalburgi, Dabholkar and Pansare were killed within a span of five years.
Earlier, in its status report, the Karnataka Police had told the apex court that it seemed there was a connection between the killings of Kalburgi and that of Lankesh in 2017.
( With inputs from IANS )