Whitbread confirmed it had added pork to a dish served in Table Table and Whitbread Inns restaurants, but denied claims in the Sun that it had continued to advertise it as a "beef lasagne".
The chain said although online menus had not been immediately updated, menus in "all restaurants" had been changed.
A spokesman said pork was part of "a traditional Italian lasagne recipe".
According to the Sun, which carried the story on its front page on Tuesday, the restaurant outlets did not change some of their menus for three months after pork had been added to the recipe.
The newspaper said the dish was still being advertised as a "beef lasagne" even though it had pork in.
The paper said the move could offend Jewish and Muslim customers, who do not eat pork for religious reasons and could have ordered the dish in the belief it contained only beef.
A Whitbread spokesman confirmed it had changed its recipe in the restaurants in September, saying "most people will be aware a traditional Italian lasagne recipe would typically include a beef and pork ragu".
"We mistakenly, and with no ill intent, missed updating the website/online menus for our Table Table and Whitbread Inns brands, but as soon as we were alerted to this we corrected them," the spokesman added.
"This was a genuine mistake on our part and we sincerely apologise to customers if this resulted in any confusion when they were presented with the correct menu at the restaurant."
However, the firm denied it had misled customers.
"We strongly refute the Sun's claim that we have added pork to our lasagne recipe at our restaurants without telling customers," the spokesman added.
"We believe that the Sun are using an old menu which has not been in use in our restaurants for some time.
"We changed the menu from 'beef lasagne' to a more authentic 'lasagne' recipe that includes pork in September last year and, at that point, we updated the menus in all of our restaurants to reflect the change."
It added: "We are confident, therefore, that our customers would have been presented with the correct menu when ordering their meal."
The firm's online menu now describes the dish as lasagne made "with a beef and pork ragu".
Whitbread owns 13 Whitbread Inns restaurants and 99 Table Table outlets.
A restaurant chain has apologised for failing to update its online menu after it added pork to its lasagne recipe.