Do the authors need to ask for permission from institutes/companies for including their name in acknowledgement section of their publication?
If the agency provides funding, and you are not sure about their policy, you  can always contact the person who administers your grant to find out. 

Some private foundations do have specific requests for acknowledgement. For example, I seem to remember that the Templeton Foundation likes authors to include a statement such as "The opinions expressed here are those of the author and not necessarily those of the John Templeton Foundation." 

Your grant agent can surely tell you about this. And they will almost certainly be happy to hear you are publishing something with their support.