Singh telephoned Chandy following murder of E Manoj and discussed with him the killings of political and social activists in Kerala.
"The Home Minister has expressed concern over the murder of social activist Manoj and asked the Kerala Chief Minister to take strict action to stop such political killings," a Home Ministry official said.
The Chief Minister conveyed to the Home Minister that a team of high level officials have rushed to the spot to probe into the incident.
Chandy also assured Singh that he would convene an all-party meet to discuss the issue of political killings in Kerala.
Manoj was killed when an unidentified gang attacked him in politically-volatile Kannur district yesterday.
The RSS activist was waylaid on a road by the gang which threw a country-made bomb at him and then hacked him to death before fleeing from the area, police said.
RSS-BJP leaders alleged that the CPI(M) was behind the killing and gave a call for a dawn-to-dusk hartal in the state today.