Does an individual working for a foreign government in India have to pay taxes on their income earned in India?

​Yes, individuals employed by foreign governments in India are required to pay taxes on their income earned in India, as salaries paid by foreign governments to their employees working in India fall under the head "Salaries" according to Section 15 of the Income Tax Act, 1961. 

However, non-Indian citizen enjoy exemption on such income. Exceptions apply when a citizen of India renders services outside the country and receives a salary from the Government of India, which is then taxable as salary deemed to have accrued in India.​