The present invention provides stabilized prolonged release pharmaceutical compositions comprising atypical antipsychotic drug like paliperidone or pharmaceutically acceptable salts thereof without incorporating surfactant and for 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.