The lines are the 24-km long Metro 5 corridor linking Thane-Bhiwandi-Kalyan in adjoining Thane district and the 14.5-km long Metro 6 corridor connecting Lokhandwala-Jogeshwari-Vikhroli-Kanjurmarg in the Mumbai suburbs.
Metro 5 with 17 stations will be built at a cost of Rs 8.416 crore and Metro 6 with 13 stations will cost Rs 6672 crore.
Both are expected to be completed within the next four years, Fadnavis said.
The decision was taken at a meeting of Mumbai Metropolitan Region Development Authority (MMRDA) presided over by the Chief Minister.
The Maharashtra Information & Technology Corporation will carry out the on-ground work to identify the 500 hotspots in the first phase under the aegis of Directorate of Information and Technology.
This is the second major metro lines project announced by the state government in barely three weeks.
On September 27, the government approved two new metro corridors - Metro 2B and Metro 4 - with an investment of Rs 25,525 crore.
Metro 2B will be 23.5 kms long linking DN Nagar-Bandra-Mankhurd and Metro 4 will connect Wadala-Ghatkopar-Thane-Kasarvadavali, both likely to be operational by 2021-2022.
Presently, Mumbai is served by the 11.4-km long Metro linking Versova-Andheri-Ghatkopar since June 2014.