INZ area manager Darren Calder said Kandel was the principal applicant for residence visa lodged in April 2013.
The application included her partner and younger son, Saphal, now 7, but not the elder Santosh.
In May 2014, an application for residence on behalf of Santosh was lodged under the Family Category.
"His application was declined because he has a condition which is deemed to impose undue costs or demands on New Zealand's public health system," Calder said.
"He was also not eligible for a medical waiver because he was not included in his mother's previous application."
Calder said the independent Immigration and Protection Tribunal had also dismissed a appeal against the decision to decline residence.
The tribunal said assessors determined that if Santosh moved to New Zealand, he would qualify for funding under the Ongoing Resourcing Scheme.
"This was estimated to be $17,000 per annum and he would be eligible for funding until he turned 21 years," it said.
"This represented significant costs to New Zealand's special education services."
Santosh has a condition that had been identified as a spastic diplegic type with global developmental delay.
He had multiple problems, including an inability to walk or communicate and required assistance with daily activities.
A paediatrician noted that he would require physiotherapy and speech therapy, hearing aids and glasses, and would need 24-hour assistance.
"The family's decision to migrate to New Zealand without him has given rise to his long-term separation from his immediate family," the tribunal added.
"How the family now makes further arrangements for their disabled son is a matter they will need to address."
It also deemed that there were no special circumstances to warrant consideration by the Minister of Immigration for an exception to residence instructions.
Santosh is currently being cared for in Nepal by his maternal grandparents.
Kandel has not seen her son since she moved to New Zealand in search of a "better life" six years ago.
"I wanted to settle down first and make sure I had the means and ability to support him before bringing Santosh over," she said.
"I know it will be a lot of work to look after him, but he is not a burden, he is my son."
The application to sponsor her son was lodged after she found herself a full-time hospitality job and jointly buying a house with her brother and sister-in-law.
Kandel had also written to INZ undertaking that her extended family would care for Santosh, but to no avail.
"In my society and culture, people live like a unit, every member of a family is looked after by the whole family," she wrote.
"In this way, he will not be a burden on New Zealand health or support systems."
Kandel said her family in Nepal had been affected by the recent earthquake and their house had been damaged.
MIGRANT HEALTH SCREENING
• Must be unlikely to impose significant costs or demands on health or special education services
• Those who do not meet requirements will be referred for assessment by medical assessor
• Will not be considered for medical waiver if they require full time care, or applying under one of the family categories
(source: Immigration New Zealand)