His comments came as Dr Haneef's legal team today pushed ahead with an application to return the former Gold Coast doctor's visa.
"The chronology is suspicious," Justice Spender said at one stage this morning.
Commonwealth Solicitor-General QC David Bennett immediately argued against the comment.
Mr Bennett said it was only the timing of the decision that was affected, not the decision itself. He said the Minister had already indicated he had taken into account the decision by the Brisbane Magistrates Court to grant Dr Haneef bail "as a matter in Dr Haneef's favour".
Dr Haneef's bail was granted on July 16 - but hours later, Minister Kevin Andrews announced he was revoking Dr Haneef's visa.
Mr Bennett also argued that media deadlines and other news events on that day may have influenced the timing of the decision.
Commonwealth Solicitor General David Bennett is working through three stages of the Commonwealth's argument against the return of Dr Haneef's visa.
Earlier this morning, he summarised the Commonwealth's argument that the best way to consider the term "association" was the Australian colloquial expression, "mate".
Justice Spender later asked if two people sharing an interest in making AFL the most popular football code in Brisbane could be considered as having a "shared interest".
Mr Bennett again referred to the term "mate", as the best way of explaining the meaning of "an association."
He said the Minister never simply relied on the fact that Dr Haneef was second cousins with Kafeel and Sabeel Ahmed.
"That is not what the Minister said," Mr Bennett said.
Solicitor Peter Russo, absent for yesterday's hearing with an upset stomach, has appeared today as part of Dr Haneef's team.
The hearing continues in the Federal Court in Brisbane in the Commonwealth Law Courts in North Quay.