Pakistan's nuclear program is a "matter of its national defense and security which falls exclusively within its domestic jurisdiction and is therefore not to be called into question by any court, including the ICJ," the foreign ministry said in a statement.
It said Pakistan had submitted a written response to the court, seeking the dismissal of the case.
Initial court proceedings began Monday, when the ICJ began determining whether it can accept the Marshall Islands' case, which aims to breathe new life into disarmament negotiations.
The Marshall Islands filed a case against nine countries that have declared or are believed to have nuclear weapons, but only the cases against Britain, India and Pakistan reached this preliminary stage.
Pakistan became a declared nuclear power in 1998, when it conducted underground nuclear tests in response to those carried out by its rival and neighbor India.