No. माता-पिता is literally 'mother-father'.
For mothers, you can say माताएँ. Fathers is a little more tricky because पिता doesn't have a distinct plural form so the workaround would be something like दो पिता (two fathers).
Your questions got me thinking and after some quick googling, it does seem that some people are definitely using माता-पिता for same-sex parents. I presume the coming years will see a consensus forming and the addition of some new vocabulary to the language. After all, gay sex was legalised in India just last year and it might take a while before the roadblocks that impede gay couples from adopting children are removed.