A special Biman Bangladesh flight carrying the prime minister and her entourage took off from the Dhaka airport at 9am on Sunday.
The Boeing 77-300 aircraft is expected to land Vienna around noon (local time) on Monday.
During her two-day official visit, Hasina is also scheduled to meet Austrian President Alexander Van der Bellen and Chancellor Christian Kern.
On the first day of her visit, the prime minister will attend a reception hosted by Bangladeshi expatriates in Europe.
On Tuesday, Hasina will attend the inauguration of the IAEA conference of at the Vienna International Centre.
Leaders from Africa, Asia, Europe, South America and the Caribbean are expected to join the conference 'International Conference on the Technical Cooperation Programme: Sixty Years and Beyond – Contributing to Development'.
After the summit, Hasina is scheduled for a meeting with IAEA Director General Yukiya Amano at the conference venue.
Foreign Minister AH Mahmood Ali, who is accompanying the PM, told the media on Sunday that Hasina's participation will reaffirm Bangladesh’s commitment to world peace.
Her participation will also “brighten” the country's image, he said, as Bangladesh always pursues peaceful use of atomic power.
Bangladesh became member of the IAEA in 1972. The prime minister’s husband, late nuclear scientist Dr MA Wazed Miah played a key role to get the membership.
Later on Tuesday, the prime minister will join bilateral talks with Austrian Chancellor Christian Kern, before which the two leaders will have a one-to-one meeting.
The Bangladesh foreign ministry said agriculture and livestock cooperation, direct flight and regular diplomatic consultations would be some of the areas the prime minister will discuss, apart from trade, investment and sustainable development.
A MoU is also expected to be signed between the countries to hold regular diplomatic negotiations between, Bangladesh Foreign Minister Ali told the media in Dhaka.
Hasina's Austria visit ends with the meeting with President Alexander Van der Bellen on Tuesday afternoon.
She is expected to leave Vienna in the evening and reach Dhaka on Wednesday morning.