State minister for foreign affairs Shahriar Alam received her at Hazrat Shahjalal International Airport in the evening.
Foreign Ministry officials said the West Bengal Chief Minister would witness the signing of documents on Land Boundary Agreement (LBA) to be exchanged between the two countries after talks between Modi and his Bangladeshi counterpart Sheikh Hasina tomorrow.
Bangladesh media prominently reported her Dhaka visit. Chief Ministers of other Indian states bordering Bangladesh are expected to accompany Modi during the tour.
Foreign Ministry officials earlier said she preferred to stay in a separate hotel, though the Pan Pacific Sonargoan Hotel is booked for the Indian premier's entourage.
The West Bengal Chief Minister appeared to have stood in the way of inking of a crucial deal over sharing of the common Teesta River at the last minute during former premier Manmohan Singh's Dhaka tour in 2011.
Ahead of Prime Minister Modi's Bangladesh tour, India made it clear that the Teesta deal would not be signed during his visit this time as India was yet to reach an internal consensus on the matter.
India made it clear that the Teesta deal would not be signed
During her previous Dhaka tour in February this year, Banerjee, however, assured Hasina of playing a "positive role" in resolving the outstanding Teesta river issue to protect interests of both sides.
Foreign relations analyst Professor Imtiaz Ahmed, however, said Banerjee's plan to visit Bangladesh separately did not necessarily indicates any negative notion.
"If Mamata stays in Dhaka during Modi's visit that is 'good enough' her decision to come separately may be linked to her preoccupation at home or she may show shes not like other chief ministers," he said.
The West Bengal chief minister, however, flagged off the new Kolkata-Dhaka-Agartala bus service ahead of her arrival calling it as "historic" step that would bring the people of Bangladesh and India together and strengthen the relationship between the two countries.
Banerjee would join the two premiers at the flag-off of Kolkata-Dhaka-Agartala bus service at the Bangladesh prime minister's office tomorrow.