The high street pharmacy chain Boots has admitted it was wrong to use separate in-store signs labelling girls' and boys' toys – putting Science Museum-brand toys in the latter category – after shoppers took to Twitter and Facebook to accuse the retailer of sexist behaviour.

In a statement posted on Facebook on Tuesday it said it was taking steps to remove the signs and that it was dismayed by customers' reaction to the move.

"It was never our intention to stereotype certain toys. It's clear we have got this signage wrong, and we're taking immediate steps to remove it from store."

Shoppers criticised the gender differentiation, also expressing their disappointment that the popular scientific toys produced by the Science Museum (and available through other retailers) had been designated as suitable only for boys.

Boots initially defended its position on Facebook (it is currently inactive on Twitter) saying that marketing science toys to boys was not stereotyping but designed to make their shops "easier to navigate" and was due to "customer feedback".

Author Megan Peel, the mother of a 10-month-old girl, told the Guardian she had emailed Ian Blatchford, the director of the Science Museum, to make him aware of how Boots was marketing the toys. "He replied within 10 minutes, copying in the head of trading and asking him to investigate immediately. He also mentioned that they had a large festival celebrating women in science recently so he very much sympathised with our concerns."

Peel said: "I know that Boots is not the only retailer to stereotype children's interests in this way, but I find it particularly disappointing that as a science-based company, who employ many female scientists, they chose to label Science Museum toys as 'for boys'. I know that I am not alone in feeling deeply frustrated by the 'pinkification' of products marketed at girls, and I believe that there is a real opportunity for retailers to win brownie points with mums by publicly pledging to treat their daughters' aspirations with more respect from now on."

The Science Museum said: "Science Museum Enterprises is committed to producing products which appeal to both genders. We are pleased to hear that Boots are updating their display to reflect this in their stores."

The row follows growing sensitivity about toys being marketed on gender grounds. In December 2011 Hamleys dropped its traditional labelling by gender and replaced old-fashioned pink and blue signs with neutral red and white ones. Toys are now categorised by type, such as arts and crafts, dress-up and dolls, without specifying whether they were for boys or girls. Last year Harrods opened its Toy Kingdom without specifying gender for its products.

In its statement, Boots said: 'We've always been proud of supporting women in science and in particular in their careers in pharmacy, and we were dismayed that our attempts to help customers shop at our store hasn't worked in the way we wanted it to. It was never our intention to stereotype certain toys."

It said science toys were sold on the Boots website by gender, age and type "to make it as easy as possible for customers to find what they are looking for".