The company uses the Pay As You Earn (PAYE) system to pay income tax and national insurance contributions which are taken off your salary before it is paid to you. Your employer is responsible for sending the tax on to HM Revenue and Customs (HMRC).
HMRC uses a tax code to tell the company what to deduct from your salary. If HMRC does not have enough information to issue a full tax code, the company will be told to use an emergency tax code until more information is received and the tax code can be adjusted.