A father has lamented the loss of two Yarra footbridge "love locks" dedicated to his young daughters, penning an emotional letter to Melbourne's lord mayor.

Kevin Neville, from Southbank, has written to lord mayor Robert Doyle about the decision to remove thousands of lovingly attached padlocks from the bridge between Southbank and Flinders Street Station.

Mr Neville and his daughters, aged two and three at the time, attached two locks to the bridge in 2013, with the words: "Daddy and I. Together Forever" written on each lock.

On Wednesday morning, workers began removing the locks after the Melbourne City Council said the locks were dangerously weighing down the safety barrier wires.

In recent years, couples and families have shown their love for each other by inscribing messages on padlocks, attaching them to the wires on the bridge, and throwing the keys into the Yarra River.

The letter begins: "You seem a man of great integrity. But my children and I have a little bone to pick with you. You stole our love locks!"

Mr Neville sees his daughters only once a fortnight and says they revelled in the opportunity to visit the locks, which cost $80 each.

"I actually walk over the bridge two times a day to and from work, and when I see my little girls' locks it reminds me to never give up trying to be a part of their lives," he wrote.

"It was nice to know that my little girls had a place in Southbank which they share with their dad."

The distressed father said not all of the locks had been attached by "lovestruck teens or tourists", and that some were put in place in memory of lost loved ones or family members.

Mr Neville said it was hypocritical of the council to remove the locks, when it had previously decorated the bridge with hearts on Valentine's Day.

The council has not confirmed what will happen to the locks.

The bar beneath the bridge, Ponyfish Island, suggested the locks could be part of its major refurbishment. Other ideas included melting them down to form a public art installation.

But Mr Neville said he did not wish either fate upon his locks. He wants them to be returned, and said his family were not given the chance to collect the locks, which he still had the keys for.

"They are ours, they are not yours, and you have stolen them from us."