Delhi Deputy Chief Minister Manish Sisodia is the second minister from the Aam Aadmi Party (AAP) to be arrested by a central agency in less than a year.
Mr Sisodia's colleague and Delhi Health Minister Satyendar Jain was the first AAP minister to be arrested by a central agency in May last year.
The AAP has accused the BJP-led centre of using the Central Bureau of Investigation (CBI) and the Enforcement Directorate (ED) to harass them.
Mr Sisodia and others face corruption allegations in bringing a new liquor sale policy in the national capital. Lieutenant Governor VK Saxena had ordered the CBI probe last year. The Delhi government reverted to the old liquor policy and blamed the Lieutenant Governor for loss of revenue worth crores of rupees.
Mr Sisodia was arrested by the CBI after eight hours of questioning today.
Mr Jain, however, was arrested by the ED in an alleged money laundering case. The probe agency alleged that the minister in the Arvind Kejriwal government was involved in hawala transactions with a Kolkata-based firm in 2015-16.
A hawala system involves two parties transacting money with local agents on their behalf without the funds actually passing through formal banking channels.