Hasn't  this become a 9 year contract already?
...
What kind of a proof can I give to commune to prove that the contract is extended?

It has indeed.
Unless it's foreseen differently in the rental agreement, it becomes a 9 years contract.

The city employee is mistaken, but no need to argue about it. Just send an email to your tenant, confirming that the rental agreement is well and legally extended.

We have signed a rental contract with my tenant with following template last year.
https://www.pim.be/telechargement/baux_ … 2014v4.pdf

The rental property is in Brussels capital region. The contract we initially signed was for one year.
This one year rental contract ended last month September 2018. Neither myself nor the tenant gave any termination notice.
Tenant wants to continue staying and we are ok with it. When tenant went to the commune, commune asked for rental contract extension proof

Hasn't  this become a 9 year contract already? How can we extend this contract to let it become a  3 or 9 year contract? Do we need to add any addendum to the original contract to signal this contract has been extended?   Strike of present date 31/9/2018 and put a new date in original contract ? Do we need to register the contract for every extension? What kind of a proof can I give to commune to prove that the contract is extended?               

BTW, I have just  sent them a letter(PIM template for rent indexation) in French, increasing the rent by 15€. Can that be a proof that the contract has been extended?

Thanks