Dougherty said the disclosure requirements did not apply to him because his grown daughter was the actual tenant at the Dockside apartments at Penn's Landing, living there for 10 to 12 weeks in 2005.
Dougherty said he stayed there as well - but only as an infrequent guest of his daughter.
He said he chose to disclose his stays on the second form, the federal one - for labor leaders - out of a desire to be completely "transparent."
Federal authorities investigating Dougherty have been looking into his stay at the elegant, 16-story building shaped like a ship. Witnesses, including the owner of Dockside, have testified before a federal grand jury.
Dougherty, who chairs the Redevelopment Authority, is also required by state law to file forms disclosing lodging given to him that exceeds $650 in a year.
Shortly after Dougherty filed the state form, news reports made public a flurry of federal investigative activity involving a close friend of Dougherty's, a civic group he heads and the Redevelopment Authority.
In late January 2006, federal agents searched the South Philadelphia home of the childhood friend, contractor Donald "Gus" Dougherty.
And in February 2006, federal authorities subpoenaed records from the Redevelopment Authority.
The next month, they subpoenaed records from the Pennsport Civic Association. John Dougherty is its president.
(Gus Dougherty recently pleaded guilty to 98 criminal counts, but is still to stand trial on charges he provided illegal benefits to John Dougherty. John Dougherty has not been charged with any crime, and has said he has done nothing wrong.)
Yesterday, John Dougherty said the federal investigative activity in early 2006 had no bearing on his decision to disclose additional information in his filing later that year.