Here is the solutions for my problem, i've used javascript calls to achieve this.
var viewPoint:Number = ExternalInterface.call("eval", "window.pageYOffset");
var browserHeight:Number = ExternalInterface.call("eval", "window.innerHeight");
//the following calculation finds the center y coordinate in user's viewable page.
var viewableY : Number = ((browserHeight/2)+viewPoint-50);
var alert : Alert = Alert.show("Error Msg");
PopUpManager.centerPopUp(alert);
alert.move(400,viewableY);
I hope this helps someone...