High Court Judge George Odunga announced that the application of eight sections of the new anti-terrorism law would be suspended because they raised concerns over human rights.
The move follows a legal challenge by Kenya's opposition, who had argued that the east African nation was at risk of becoming a dictatorship.
The security bill was passed by parliament last month after a debate that sparked brawls between governing coalition and opposition MPs, and was signed into law by President Uhuru Kenyatta.
The suspended clauses include the threat to journalists, a ceiling on the number of refugees allowed to be in Kenya, as well as definitions on what constitutes support for terrorism.
The government argues the measures are necessary to confront a wave of attacks by Somalia's Al Qaeda-affiliated Shebab insurgents, and that amendments giving the courts more oversight over the police and intelligence services make it constitutionally sound.
