As per provision Sec 200(3) ie filing after due date. it explianed that non compliace of this sec will attract penalty
1)u/s 271A(2) of Rs 100/- day for tax deductible upto 30/06/2012. and
2) fees of Rs 200/- day of default u/s 234E for tax deductible on or after 01/07/2012 the first point i.e 271A(2) is not applicable because it replaced by 234E. and
3)penalty under sec 271H minimum Rs10000/- to max Rs 100000in respect of tax deductible on or after 01/07/2012.
so as per your query u said whether u can waive penalty u/s 234E.
since sec 234E is not penalty it a fees which is to be paid to central govt. so it connot be waived off.
you can waive off penalty under 271H. by