The photos of children waving the inaccurate flags at the presidential palace on Wednesday have caused an outcry in Vietnam.
Mr Xi was on a three-day visit to Vietnam aimed at strengthening ties between the neighbours.
Vietnamese authorities have yet to comment on the matter.
The flag of the People’s Republic of China is red with four small yellow stars surrounding one larger star on the upper corner near the flag pole.
Messages on online forums in Vietnam have demanded an explanation. One blogger said it was a “terrible diplomacy error”. Some have also asked why China has not questioned the flag faux pas.
An inaccurate Chinese flag also appeared on a news programme on Vietnam’s VTV1 channel in October.
A similar incident also happened during a welcoming ceremony for an official Chinese delegation in Delhi in 2006, where the Chinese flag also had six stars instead of five.