My 1099R from NYS ERS says it is exempt from state tax but when I enter it tax due increases. Is this correct?

The NY tax  may increase when you first put in the 1099-R, but you also need to carefully step thru ALL of the questions that follow the main 1099-R form.  There is one (shown below ... but may be a bit different this year) where you need to indicate which pension system the 1099-R came from.  After doing that, it should limit the NY taxes...assuming you are a member of one of the eligible NY retirement systems.

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also, are you a NY state resident?  If no, then it may be taxable in the state you now reside in.  

ooooh.....good point must be a NY resident at the time you receive the $$ to get the exemption.