He made his comments at the Gardaí (Irish police) and PSNI's annual cross-border seminar on organised crime.
Mr Storey, the northern chairman of Sinn Féin, was later released without charge.
Mr Hamilton said he was confident that police had acted with "integrity".
"I am confident that the meetings and the co-operation with An Garda Síochána, with the commissioner, is positive, is healthy, we're in the same place," he said.
"Our efforts are combined in trying to keep people safe and to reduce this threat."
Mr Storey was one of three leading republicans questioned and then released without charge over the murder of former IRA man Kevin McGuigan Sr.
Mr Storey's arrest intensified a political crisis in Northern Ireland.
It was triggered when police said they believed IRA members had been involved in the murder of Mr McGuigan in Belfast in August.
Chief Constable George Hamilton said the IRA was still in existence, but added that the organisation was not engaged in terrorism.
Following the murder, Sinn Féin said the IRA no longer exists after it ordered an end to its armed campaign in 2005.
The claims by Mr Hamilton led to a breakdown in trust between Sinn Féin and unionist parties.
The Ulster Unionists withdrew from Northern Ireland's ruling executive, with three Democratic Unionist Party (DUP) ministers also later resigning, and DUP leader Peter Robinson stepping aside as first minister.
Unionists agreed to join the talks when the government ordered an independent review of paramilitary groups in Northern Ireland earlier this month.
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The Chief Constable George Hamilton has defended the PSNI's actions over the arrest of Bobby Storey as part of their investigation into the murder of Kevin McGuigan.