I'm assuming you don't need recommendations for active established artists like ayaka, BENI, Miliyah Kato, MISIA, miwa, Leo Ieiri (not that I would recommend her anyway, I haven't liked a song of hers in a few years)... I don't know what kind of music you're into, but I'll try to list any slightly less prolific female artists I think are worth checking out.
Aimer
She's really blown up over the last few years, so you've probably heard of her already. She's a versatile artist who mostly does different flavors of pop-rock, and she has a pretty extensive discography already, so I'm sure you'd find something you like.
Sailing
ONE
us
eill
She's indie, and she only has one album out, but I would recommend checking that album out! She's a promising modern pop artist.
MAKUAKE
FUTURE WAVE
iri
A low-voiced singer-songwriter who makes hip-hop influenced R&B/pop music. She's going to release her third album, Shade, in two weeks!
Shade
Corner
Watashi
rhythm
KIRA
She's an hip-hop/reggae-influenced singer-producer.
SPACEY LOVE
Nadeshiko SOUL
JEALOUSY
Mirei Touyama / MIREI
She's an amazingly talented young R&B singer.
Negai ~Ano Koro no Kimi e~
My Way
NakamuraEmi
She makes acoustic hip-hop-pop. She's a really fun artist, one of my favourites to follow in the last few years! And she just released her fourth major-label album, NIPPONNO ONNAWO UTAU Vol. 6, today! (Though if you're going to listen to more of her, I'd recommend starting with NIPPONNO ONNAWO UTAU Vol. 4 or NIPPONNO ONNAWO UTAU BEST).
Ame no you ni Naiteyare
Major Debut
YAMABIKO
RIRI
Another young R&B-pop singer, she has a more modern and global take on the genre (she kinda seems to want to be the Japanese Ariana Grande).
HONEY
Maybe One Day
Seiko Oomori
I've seen her labeled an "anti-idol"; I'd probably describe her as a successor of Shiina Ringo, bringing an intense, challenging, unpolished rock edge to mainstream pop.
Shinigami
TOKYO BLACK HOLE
Shishido Kavka
She's not the most active artist, but she's been releasing albums steadily since 2013. She's a singer-drummer who makes energetic pop-rock music.
Bane no Uta
Love Corrida
yanaginagi
She's a soft-voiced singer-songwriter who came up through the utaite scene on NicoNico. She is currently signed on NBCUniversal and is firmly in the anison ghetto, so you may not have heard of her though she's been releasing her sweet pop-rock (and occasionally some off-the-wall stuff) on a major label since 2012. She just released two best-ofs, LIBRARY and MUSEUM, at the beginning of this year.
Meimoku no Kanata
Sweet Track
Tokohana
Mitsuba no Musubime
And if you feel like branching out to female duos/acts with a female frontwoman...
Haruka to Miyuki
They're a female alt-rock duo who have made some varied and powerful rock music.
(Most of their stuff is blocked from YouTube because Sony Music Japan is a hateful entity that plagues us international J-pop fans.)
Kiseki wo Inoru Koto wa mou Shinai
Vanilla
Inshow-ha
They're a female indie pop-rock duo. Their style is really cool and a little quirky.
Lemon
Kiss! Kiss! Kiss! One More Kiss!!
BEAM!
Suiyoubi no Campanella
They're a trio where the female singer, KOM_I, is the only member who really appears in public, so it might as well be her solo act. They make cutting-edge genre-blending music mainly influenced by electronica, dance pop and hip-hop, and they are famous for their quirky lyrics, interesting videos and unorthodox live performances. Please please please check them out.
Kaguya-hime
Melos
Aladdin
Unico
Medusa
Diablo