Dear Ahsan
As stated by you that joints in masonary are up to 3 cm. The thicker joints reduce the strength of masonary. If you use coarse sand in the mortar , ratio of cement mortar was rich and proper curing was done than the effect is negligible. You are stating that sand filling is in progress than outer face of the masonary should be checked and after cleaning the joints do plaster with cement and coarse sand in the ratio 1;3 or 1;4, do proper curing, this will also protect from water logging. If you laid plinth beam than it is OK, if not laid than lay now which will not only strengten the masonary but also a good measure against earth quake.