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The College also offers courses leading to a Masters Degree in Science subjects such as M.Sc. : Organic Chemistry, ComputerScience, Electronic Science , Physics; M.Sc.Tech : Industrial Maths with Computer Applications, and M.C.A: Master of Computer Application. There is an increasing interaction with industry through the Computer Science, Electronic Science, and Chemistry Departments.

Post Graduate Centre in Chemistry: M. Sc. (Organic Chemistry) (Non -grant basis)

The Dept. of Chemistry, Fergusson College conducts a 2 year full time M.Sc. programme in Organic Chemistry. Total seats available are 48. The admission is through an entrance examination at Department of Chemisty, Fergusson College,Pune.Results of all batches since the course was initiated in 1994 have been excellent and students get placements in Chemical or Pharmaceutical companies and research laboratories.
Post Graduate Centre in Electronic Science (Non-grant basis)

M. Sc. Electronic Science gives the opportunity to assimilate the wide range of disciplines required for a challenging career in Electronics and Instrumentation. Following the first two semester common core, the third and fourth semester of this degree offers a range of options which take the students to the leading edge of technology. The Department provides the following specialized courses:
- Digital logic design
- Micro controllers
- PC-based Instrumentation
- Digital Signal Procesing
- Communications & Networking
- Embeded System
- Industrial & Power Electronics
- Robotics
- CAD/CAM and Industrial Process Control
Specific research groups in the department present these options with material approaching the state of the art technology of current interest to industry.
Post Graduate Centre in Physics
Fergusson College post graduate centre in Physics (estd 1969) is approved by the State Government and the Pune University. The intake capacity of M.Sc. part I is 33. Post graduate Course in Physics consists of four semesters (Two Years). Pune University conducts theory and practical examinations at the end of each semester.Admissions to M.Sc. (Physics) are given by the college as per rules and regulations of Pune University.

Admission forms are available after the T Y. B.Sc .results are declared The following departmental papers are offered at M. Sc. (Physics).
1. Digital Electronics
2. Microprocessors
3. Radio Communication and T. V.
4. Industrial Electronics
5. Network Analysis
6. Communication Electronics
7. Physics of Semiconductor Devices
8. Vaccum Technology and Thin Film Physics
9. Material Science
10. Astrophys/cs and Astronomy
11. Lasers and Laser Applications
12. Atmospheric Physics
13. Renewable Energy Sources
The Physics Department has research collaboration with INTA, Spain. This is one of the global centres monitoring the minor constituents of the atmosphere. An EVA spectrometer is installed in the Post Graduate Physics Laboratory.