Instead, it will be used to assess the impact of immigration on schools.
Schools in England were asked to start collecting this information in September, leading to fears it may be used to find illegal immigrants.
Campaigners have written to Education Secretary Justine Greening to ask her to axe the data collection plans.
A Department for Education spokeswoman said: "Collecting this data will help ensure our children receive the best possible education.
"It will be used to help us better understand how children with, for example, English as an additional language perform in terms of their broader education, and to assess and monitor the scale and impact immigration may be having on the schools sector.
"Data on pupils' country of birth, nationality and level of English proficiency is collected through the school census in line with the national population census.
"These data items will not be passed to the Home Office.
"They are solely for internal Department for Education use for analysis, statistics and research."
An earlier letter to Ms Greening from at least 20 organisations said: "Without assurances to the contrary, our grave concern is that the new data collected will be shared with the Home Office and therefore potentially used for immigration enforcement purposes.
"We have already seen data sharing between the Home Office and other departments increase since the government announced its commitment to creating a 'hostile environment' for undocumented migrants.
"Such measures deter vulnerable children and families from accessing essential services, exercising their human rights, and participating on an equal basis in our communities."
Under the new expanded census, schools are, for the first time, asking parents to say which country their child was born in.
Disclosure is not compulsory, but a report by Schools Week found many schools were demanding copies of pupils' passports amid confusion about the new stipulation.
Gracie Mae Bradley, from Against Borders for Children, which is leading the campaign to have the policy overturned, urged parents to boycott the data collection.
She said: "School should be a place where all children are treated equally.
"In the context of a 'hostile environment' in which employers, landlords and even healthcare workers are being turned into border guards, we believe this new requirement could be used to add school administrators to the list.
"We are also deeply concerned that this data will be made available, without time limit, much more widely outside the schools system, which cannot be acceptable.
"Over the coming weeks we expect the organisations opposing this divisive approach to be joined by many more and for parents and schools to join the boycott and protect young people from this dangerous threat to their privacy."

The details are contained in an official analysis of the budget by the Department for Social Development (DSD).
The analysis suggests the average loss per household will be £918 per year.
Tax credits are effectively a means-tested benefit paid to people on lower incomes.
They are paid to two main groups: unemployed people with children and low paid working people who may or may not have children.
The changes to tax credits in the July budget included lowering the threshold at which payments start to reduce.
Currently tax credits payments start to reduce, or taper, once a family income reaches £6,420.
From April 2016 the threshold at which payments taper will be £3,850.
There are currently 109,000 claimants in Northern Ireland who are earning above the £6,420 threshold and have a 'tapered' tax credit award.
Once the threshold is reduced to £3,850, these claimants will have their tax credit award tapered further.
An additional 12,000 claimants will also become subject to the taper once the threshold is reduced to £3,850.
The DSD analysis also looks at other welfare changes announced in the budget, including the freeze in most working age benefits up to 2020.
Using an assumption that welfare reforms will ultimately be introduced in Northern Ireland, it estimates that the July budget will take £206m off the welfare bill in 2016/17, rising to £361m in 2019/20.
The DSD analysis does not factor in the impact of the National Living Wage or increased personal tax thresholds on household budgets.

The Stags have an option of signing a permanent deal with the 22-year-old striker.
Coulthirst, a graduate of Tottenham's academy, made just one first-team appearance while at White Hart Lane.
The striker also had loan spells with Leyton Orient, Torquay, Southend, York and Wigan.
Coulthirst will join his former team-mate Hayden White at Field Mill, after he was signed on loan from Posh a week ago.
Find all the latest football transfers on our dedicated page or visit our Premier League tracker here.
Data on pupils' nationality now being collected by schools will be not passed to immigration officials or the Home Office, the government has said.
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More than 120,000 households in Northern Ireland will have their tax credit payments reduced as a result of the July budget.
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League Two side Mansfield Town have signed Peterborough United forward Shaquile Coulthirst on loan until the end of the season.