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National Insurance calculation after 52 weeks exemption ends mid month

I have searched for this online and just cannot find an answer to my situation. 
I arrived in the UK on a Tier 2 ICT visa on January 27th, 2019. I am paid on a monthly basis at the end of each month. As I was eligible for exemption from National Insurance contributions for a period of 52 weeks, my employer did not deduct any amount for NI till December 2019.
However in my salary at the end of January 2020, a deduction has been made for NI on the basis of my salary for the whole month of January. My question is that since I was exempted for a period of 52 weeks, shouldn't the salary being considered for NI deduction only include the income for the last 4 days of January (i.e. the days after my exemption period had elapsed). 
My employer has advised me otherwise and said that the salary for the whole month would be considered. I was also told that the NI deduction in my January 2020 salary would have been the same had I arrived at any time between January 1st 2019 - January 31st 2019. Is this correct? If so, does it not imply that I am not getting the exemption for the full 52 weeks?
I have tried to scan through the information on UK GOV site as well but am not able to get any clarity for such a situation. Any help would be greatly appreciated.
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