JAVA in loop leading to errors caused by memory loss (and other things)

I have a program which creates JAVA objects within a loop. After every iteration the command

   clear java

is used. After running for 10 or more hours, with each loop taking about 60 seconds, the program returns errors seemingly caused by memory overflow. It also occasionally returns errors relating to comanly used matlab functions like

pause()

save()

Is the clear java command sufficient to free all memory used by java objects? If it is not, are there any functions that would? If it is what else could be causing these errors?