Tyres were burned and barricades set up to prevent vehicles from passing.
The nationwide strike was called by Hefazat-e-Islam, which translates as Protection of Islam. Many Islamist groups in Bangladesh accuse Modi of alienating minority Muslims in Hindu-majority India.
At least five people were killed and dozens injured in police gunfire in eastern Bangladesh on Saturday, a hospital doctor said.
Security forces were trying to quell protests against Modi's visit.
Activist Abdullah al-Munir said the protest had been peaceful.
Modi arrived in Bangladesh on Friday, his first international trip since the outbreak of coronavirus.
He left the country on Saturday after holding talks with Bangladesh Prime Minister Sheikh Hasina and gifting the country 1.2 million COVID-19 vaccine shots.
- [NON-ENGLISH SPEECH]
INTERPRETER: It was a peaceful protest but during that protest many of our activists were killed and, for that, today, we have called this general strike.