I have a problem which will take 1000000 lines of inputs like below from console.
0 1 23 4 5
1 3 5 2 56
12 2 3 33 5
...
...
I have used scanf,
Use binary I/O if you can. Text conversion can slow down the reading by several times. If you're using text I/O because it's easy to debug, consider again binary format, and use the od program (assuming you're on unix) to make it human-readable when needed.
Oh, another thing: there's AT&T's SFIO library, which stands for safer/faster file IO. You might also have some luck with that, but I doubt that you'll get the same kind of speedup as you will with binary format.