One officer is a regional head of the National Criminal Intelligence Service (NCIS), while the other was working with the National Crime Squad (NCS).
They are understood to have been accused of offences connected with mishandling informers who were involved with known criminals.
A detective chief inspector from the North-east regional branch of NCIS, based in Wakefield, has been sent back to his force in Derbyshire and is currently under suspension. He is the most senior officer of NCIS, the national organisation that collects intelligence on the country's top criminals, to have been suspended after allegations of wrongdoing.
A detective sergeant from South Yorkshire Police, who was working for the northern branch of the NCS, has also been returned to his original force and has been suspended.
Both men are understood to have been accused of misusing informers and are being questioned about their connections with members of the criminal underworld.
Greater Manchester police have been called in to investigate the case. The detective chief inspector had access to top-secret and sensitive information on computer of leading criminals and key informants.
Investigators have seized documents from the homes and offices of both men.
The inquiry is believed to have stemmed from an alleged plot that involved smuggling in a large number of mobile telephones on behalf of several bogus companies. The phones were later sold on without paying VAT.
The two men were suspended on Thursday following an investigation by NCIS, NCS, and Customs and Excise.
A NCIS spokesman said the allegations were of a "serious disciplinary nature".