well, im indonesian, and ive never been to a hotel there, clean or not.

but i really wouldnt want to go to one there because to me, everything seems to be dirtier there. just my opinion [:
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well its true [:

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Cheers
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Hotel Bumi Kersa in Pancoran suburb of Jakarta is quite affordable, priced at US$50 per room per night. For the price, it's a wonderful place.

You can view the hotel at http://www.bidakara.co.id
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stayed there

There is a very nice guesthouse named Guntary in West Jakarta.
Very clean, comfy and homy, and crazily cheap!
You've got bed with full bedding, TV, AC, private bathroom, hot water, and even breakfast for only ca. $9!
The staffs are very nice and polite too.

Address:
Jl. Merpati no. 2 Raya Penggilingan (near Walikota of East Jakarta / Walikota Jaktim)

Ph. 021-91675998, 94497903, 4804732
References :
Stayed there

try Alila Jakarta. its very cheap, but the hotel is very very nice. not 5 stars, and the president suit room is huge enough, but the price is even lower then the standard room of 5 stars hotel. ive stayed there. but location sucks. not at central jakarta. kinda remote for tourists or foreigners that dont really know jakarta
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You can try http://www.hotelbooklet.com which compares more than 30 popular hotel reservations sites and shows the cheapest rates in Jakarta!
References :
http://www.hotelbooklet.com