Officers also carried out search warrants in Wales, Somerset, London and Surrey last week.
All three were subsequently interviewed and released on conditional bail pending further enquiries.
The federation represents more than 145,000 rank-and-file officers, up to and including the rank of chief inspector as well as special constables.
City of London Police previously said its domestic corruption unit had been investigating allegations of fraud by abuse of position in relation to the federation over the last year.
Det Supt James Halkett said at the time that detectives were carrying out a “complex and active investigation in which we are pursuing all lines of enquiry”.