The shut-down, called to protest the state government's "failure" to stop the violence against celebration of 200th anniversary of the Bhima-Koregaon battle in Pune district, disrupted normal life across Maharashtra, including Mumbai.
The shut-down was withdrawn later Wednesday evening.
As many as 182 flight departures and 53 arrivals at the Chhatrapati Shivaji International Airport (CSIA) were delayed till around 4pm, according to a website tracking realtime flight status at airports across the world.
Of the 12 cancelled flights, seven were departures and five were arriving ones, as per the website.
When contacted, a Mumbai International Airport Limited (MIAL) spokesperson said the "flights (are) landing and taking off on time".
The transferred passengers from domestic to international and vice versa were being taken to the respective terminals using the 'air-side' (internal route), the spokesperson added.
Crew members of various airlines also reported late at the airport due to traffic disruptions.
Bharipa Bahujan Mahasangh (BBM) leader Prakash Ambedkar had called for a 'Maharashtra Bandh' today to protest the state government's "failure" to stop the violence at Bhima Koregaon village in Pune district on Monday.
The event to mark 200th anniversary of the Bhima Koregaon battle in Pune district, in which forces of the East India Company defeated Peshwa's army, was marred by incidents of violence in which one person was killed.