BJP Kerala state president Kummanam Rajasekharan told the media that Shah could not participate in the party march as he had to attend a meeting with Prime Minister Narendra Modi.
The rally on its third day was between Mambaram and Thalassery via Pinarayi.
BJP claims that ‘Janaraksha Yatra’ is being organised by the party to create awareness among people of Kerala against ‘red terror’.
Shah earlier had said that the rally is being organised to protest the political murders being carried out by the CPI (M) in Kerala.
Hundreds of party workers led by the state unit chief participated in the rally. According to reports shops remained closed when the yatra reached Pinarayi.
Rajashekharan said Shah's presence in the yatra was not required to offer resistance to CPI(M) workers of Pinarayi village.
The BJP party workers also paid a visit to the house of slain RSS worker Remith at Pinarayi. Last year Remith was hacked to death allegedly by CPI (M) party workers.
Kerala party chief told the media that Shah is scheduled to re-join the yatra on Thursday.