"The president expressed understanding of Martin's decision but underscored the importance of redoubling our security cooperation efforts," White House spokeswoman Erin Healy said.
Martin announced in late February that Canada would not participate in the missile defense program, which a majority of Canadians oppose, according to polls. Martin has said he would not support the "weaponization of space," and some believe deployment of the shield could lead to an international arms race.
U.S. officials have expressed disappointment with Martin's decision.
During their 15-minute conversation, Bush and Martin "expressed the importance of our ongoing cooperation in NORAD (search) (the North American Aerospace Defense Command) to continental security," Healy said.
Martin and Bush also talked about their March 23 meeting with Mexican President Vicente Fox. Bush will hold working sessions with Fox and Martin at Baylor University in Waco, Texas, and host a lunch for them at his ranch in nearby Crawford.