The president did not express his disappointment with the decision by Martin's government in the 15-minute phone call, Martin's spokesman, Melanie Gruer, said.
Martin had called Bush Tuesday to explain his decision, but Bush did not return the call until Saturday.
Canadian media had widely interpreted this as a sign of US dissatisfaction, on top of Secretary of State Condoleezza Rice putting off a visit to Canada partly as a result of the decision.
Martin's minority government has tried to improve relations with Bush, frayed badly by his predecessor Jean Chretien's decision not to back the US-led invasion of Iraq.
But he opted February 24 not to take part in the missile defense shield under heavy political pressure in Canada, where Bush and the system are highly unpopular.