HMRC guidance states that this can be done via online service but I could not find an option to do it.
Finally on calling them they informed that I need to send a letter to:
Corporation Tax Services,
HMRC
BX9 1AX
Sample letter below:
Corporation Tax Services,
HMRC
BX9 1AX
10th Jan 2017
Dear Sirs,
Sub: Company now Active
Unique Taxpayer Reference (UTR): 6666 6666 66
Company Name: THE ABC LTD
Company Number: 09000000
Please make the above mentioned company ACTIVE in your records. The company started trading from 5th Oct 2015.
Please can we request you to make the following accounting period live to enable us to file the tax return:
Period: 1st Oct 2015 to 30th September 2016.
In case you have any questions, please do not hesitate to contact us. We are their HMRC Agent. Our Corporation Tax Agent Reference is: H2102A
Yours faithfully,