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My wife has been in the uk since october 2009 she passed life in the uk test and ilr 3 years ago . Does she need to pass english test before citizenship application.

Yes, B1 level English from an approved test/test provider unless her nationality is exempt or she has a degree taught in English.

https://www.gov.uk/government/uploads/s ... entres.pdf

She has a masters degree from Pakistan in physics which was taught in english.

Then she needs to apply for the the ELA from UK NARIC and a letter from her university about the course being taught in English.