In his blessing, he prayed the council staff receive guidance and wisdom in their work, and that they be "blessed with knowing injustice, oppression and anger, so they can work for justice, equality and peace."
In his speech, Mr Scott - who Mr Duckworth joked had been let out of the Beehive for "good behaviour" - praised the "team effort" of St Marks and the council to "make the community strong."
"It's really positive that these guys are working together to help those who have fallen through the cracks," he said.
"It's better when our community work together - rather than beating each other up, trying to win and staying in silos."
Mr Scott, who is doing a Parliamentary induction course with his fellow new National MPs, told the Times-Age he enjoyed attending "such a positive event" after a "frantic" week in the Beehive.
Council manager Tere Lenihan said she and Rev Chalmers had been planning on working together with youth for some time.
"We were thinking a lot about how we, as organisations, can co-exist - and how the church community can reach the young people we [the council] represent.
"Involving St Mark's will help expose our young people to different kinds of cultures, and allow them to be supported by people other than our team," she said.
The council serves Wairarapa youth and their families through programmes such as Life to the Max, Big Brother, Big Sister, Alternate Education Carterton and the Rangatahi to Rangatira youth group.