The present invention provides stabilized prolonged release pharmaceutical compositions comprising atypical antipsychotic drug like paliperidone or pharmaceutically acceptable salts thereof without incorporating surfactant and/or water penetration enhancer. Such compositions are preferably in the form of a matrix wherein one or more release controlling agents are present in and/or on the matrix. Further, such compositions comprise one or more release controlling agent and exhibits desired in vitro release of drug with or without lag period. The invention also provides a process for the preparation of such compositions.