Make sure you have added the dll and the ajax registration in Bin directory and the web.config file :
1. Installing AjaxToolkit
2. Add the ajaxtoolkit.dll in the BIN directory of your website
3. Add this in the web.config inside Controls node:
<controls>
<add tagPrefix="cc1" namespace="System.Web.UI"
assembly="System.Web.Extensions, Version=1.0.61025.0,Culture=neutral,PublicKeyToken=31bf3856ad364e35"/>
<add namespace="AjaxControlToolkit" assembly="AjaxControlToolkit" tagPrefix="cc1"/>
</controls>
After this you can put the ajax control any where in your master page