The accused, Ramchander and Sandeep, worked as 'safai karmacharis' (cleaning staff) in the building.
They have been arrested for theft and the dagger has been recovered, Joint Commissioner of Police (Crime) Ravindra Yadav said today.
The incident came to light on Monday, the day the museum is closed for general public, when the museum staff found a casket in the gift room of the museum broken and the dagger, stored inside it as an exhibit, missing from its place.
Later, a case of theft was registered at Chanakyapuri Police Station here.
The case was later transferred to Delhi Police's Crime Branch, a senior official said.