Abdul Qayoom sahib, As per my limited knowledge regarding commercial construction........
1) construction materials purchase must be in YOUR control ..... It is where you start saving money in a project...... By doing so you save 200 to 400 rupees per sq. Feet so keep the whole purchase of construction materials in your own hands please..... Your 24 hours watch man must be extra reliable and must be able to measure the materials that arrives to site...... A good watchman or chawkeedar kaka would save your 2 to 5% of your project money as compared to the other typical contractors.....
2) divide your whole project in 10 items AT LEAST i.e structure work, CMU work, plaster work etc..... Give each item to a DIFFERENT labour party and on lump sum labour amount for each item........
If you would follow these tips, your 95% problems are resolved...... Good luck.....