The move is a blow to Ogilvy & Mather, which had previously been COI's sole stand-by agency.
WCRS and WTCS pitched against the incumbent and Publicis for the business.
The winning agencies will both be considered to create rapid turnaround campaigns when there is insufficient time to carry out a standard pitching process. It is the first COI assignment for WTCS since it was awarded a place on the Government roster last year.
Over the past year, O&M had created several public information campaigns including one warning of internet paedophiles and a campaign exposing the impact of the foot-and-mouth crisis.
While it had been widely expected that COI would only appoint one stand-by agency, the appointment of both WCRS and WTCS will give government departments a choice over how to approach their emergency campaign strategies.
Peter Buchanan, the COI deputy chief executive, said: "Stand-by work can be challenging for a number of reasons as we look for agencies to deliver measurable success in short time frames. We have appointed two agencies as our clients have been requesting a choice, and to introduce a competitive element, which will drive standards higher."
The pitches were overseen by a review panel which included Buchanan and various clients from other Whitehall departments.
COI had previously hired WCRS to create work for the Department for Education and Skills foundation degrees and also the Electoral Commission's Mayor of London campaign.
The majority of last year's emergency work for COI from O&M comprised press advertising. Television, radio, outdoor and internet activity formed the remainder of the campaigns.