I can find him on the 1861 census at 11 years age.
To help others looking the 1861 census
RG 9; Piece: 640; Folio: 98b; Page: 5
William J Philips 32 Portsmouth Carter
Harriett E Philips 33 Bishopstoke
William J Philips 11 Portsmouth
John R Philips 7 Landport
Henry G Philips 5
Harriett Philips 2
1871 RG10; Piece: 1127; Folio: 60; Page: 33
William Phillips 36
Harriet Phillips 36
John Phillips 18
Henry Phillips 14
Harriet Phillips 15
Elizabeth Phillips 9
George Phillips 7
Sarah Phillips 5
confirming mmn HUGHES
John Robert PHILLIPS
Birth year 1853
Birth quarter 4
Mother's maiden name
HUGHESDistrict Portsea Island Hampshire Volume 2B Page 323