They've tried unsuccessfully to get a managed isolation and quarantine (MIQ) spot via the lobby and a compassionate exemption to pick up their son.
"He's two years old. We missed his recent birthday last month," Small told Checkpoint.
"My wife applied for five or six applications online through the MIQ lottery. We've also applied for an emergency MIQ placement. However, we've been declined for that.
"We've been advised that we need supporting documentation such as maybe a police statement, a court statement or court documents, or a childcare services statement.
"I really don't want to get either of those parties involved."
He said the couple were privileged to have supportive parents who cared for the child. "They both care for him and love him, so I don't think he really knows what's going on."
Small said if only the couple could "fly back to New Zealand, pick up our son and bring him back to Australia", it would be ideal.
"Alternatively, be granted a position in MIQ so that we can be released and ... pick up our son, reunite with family and come back to Melbourne."
He described his situation as stressful and sad.
"It's stressful and frustrating for the grandparents too," he said.
He wanted the government to provide clarity on MIQ and future travel conditions.
"Give us some advice ... tell us what the plan is.
"We're both vaccinated, when can we see our son?"
Covid-19 Response Minister Chris Hipkins has outlined the plan for MIQ over the next few months.
From November 8, double vaccinated travellers from low-risk Pacific countries will be able to skip MIQ.
From November 14, returnees will only need to spend seven days in MIQ and three days at home. With tests on day zero, day three and day nine.
In early 2022, more travellers will be able to isolate at home.
Small said the prospect of not being able to see his son for another four to five months was "terrible".
"That's devastating news. I'm not prepared at all, I really just want to reunite with my son, get him back."