Mr Williamson paid tribute to the "outstanding'' use of the Automated Targeting System - Global to help with security during the Rugby World Cup last year.
"It allowed us to provide an enormous amount of security to our nation at a time when there were huge numbers of people coming through the border.''
Mr Williamson said the statement was a platform for an invigorated work programme that would support the goals of secure, facilitated trade and travel.
"It enables us to work closely together to expand our targeting work, to achieve more effective interventions with high risk persons and to facilitate legitimate travel.''
Ms Napolitano's visit coincides with the first anniversary of the killing of Osama bin Laden in Pakistan last year.
Her department was set up in the wake of the September 11 terrorist attacks on the United States.
She had been due to attend the US-NZ Partnership Forum in Christchurch last year, which was caught up in the earthquake but cancelled because of a domestic crisis.