Your code only checks whether an item in the array is the same as its immediate predecessor.
If your array starts out sorted, that will work, because all instances of a particular number will be contiguous.
If your array isn't sorted to start with, that won't work because instances of a particular number may not be contiguous, so you have to look through all the preceding numbers to determine whether one has been seen yet.
To do the job in O(N log N) time, you can sort the array, then use the logic you already have to remove duplicates from the sorted array. Obviously enough, this is only useful if you're all right with rearranging the numbers.
If you want to retain the original order, you can use something like a hash table or bit set to track whether a number has been seen yet or not, and only copy each number to the output when/if it has not yet been seen. To do this, we change your current:
if (a[k] != a[i])
a[k+1] = a[i];
to something like:
if (!hash_find(hash_table, a[i])) {
hash_insert(hash_table, a[i]);
a[k+1] = a[i];
}
If your numbers all fall within fairly narrow bounds or you expect the values to be dense (i.e., most values are present) you might want to use a bit-set instead of a hash table. This would be just an array of bits, set to zero or one to indicate whether a particular number has been seen yet.
On the other hand, if you're more concerned with the upper bound on complexity than the average case, you could use a balanced tree-based collection instead of a hash table. This will typically use more memory and run more slowly, but its expected complexity and worst case complexity are essentially identical (O(N log N)). A typical hash table degenerates from constant complexity to linear complexity in the worst case, which will change your overall complexity from O(N) to O(N2).