Sarma and his junior minister Pijush Hazarika received the students at the Sarusajai quarantine facility in the city after they arrived at 3 am by buses.
"After a long journey from Kota, 391 children are back with smiles and cheers. To ensure that they and their families remain safe, we are putting them into 14 days of quarantine," the health minister tweeted.
The boys have been kept at the Sarusajai quarantine facility and the girls in three hotels.
The students started their nearly 2,000-km journey from Kota in the west of India to Guwahati in the northeastern state of Assam on Thursday.
Kota is a coaching hub where medical and engineering aspirants from different parts of the country go every year in large numbers to prepare for competitive exams.
Quarantine has been made mandatory as the students are coming from Rajasthan which has been categorised a COVID-19 'Red Zone' and moreover, there is also the possibility of contracting the disease during the journey, Sarma had said.
The state government facilitated the return of the students in 17 buses against a charge of Rs 7,000 per person.
Swab tests will be conducted on the students on the fifth day and doctors will decide whether those testing negative can be discharged and allowed to spend the remaining nine days under home observation, Sarma had said earlier.
The students, who have already been in quarantine in Kota, have not come into direct contact with any COVID-19 patient, he had said.
The state government requested the authorities of Rajasthan, Uttar Pradesh, Bihar and West Bengal to allow their movement during the ongoing lockdown period. DG NN ANBANB